Plants Having Enhanced Yield-Related Traits and a Method for Making the Same

ABSTRACT

The present invention relates generally to the field of molecular biology and concerns a method for improving various plant growth characteristics by modulating expression in a plant of a nucleic acid encoding a GRP (Growth-Related Protein), specifically a nucleic acid encoding a HAL3 polypeptide, a nucleic acid encoding a MADS15 polypeptide, a nucleic acid encoding a PLT transcription factor polypeptide, a nucleic acid encoding a Squamosa promoter binding protein-like 15 (SPL15) transcription factor polypeptide or a nucleic acid encoding a basic/helix-loop-helix (bHLH) transcription factor. The present invention also concerns plants having modulated expression of a nucleic acid encoding a GRP, which plants have improved growth characteristics relative to corresponding wild type plants or other control plants. The invention also provides constructs useful in the methods of the invention.

RELATED APPLICATIONS

The present application is a continuation of U.S. patent application Ser. No. 12/294,983 filed on Sep. 29, 2008, which is a national stage application (under 35 U.S.C. 371) of PCT/EP2007/053081, filed Mar. 30, 2007, which claims benefit of European applications 06075822.4, filed Mar. 31, 2006; 06075823.2, filed Mar. 31, 2006; 06075918.0, filed Apr. 10, 2006; 06075957.8, filed Apr. 27, 2006; 06114140.4, filed May 18, 2006; 06117235.9, filed Jul. 14, 2006 and 07100833.8, filed Jan. 19, 2007 and U.S. Provisional applications 60/790,151, filed Apr. 7, 2006; 60/790,116, filed Apr. 7, 2006; 60/792,225, filed Apr. 14, 2006; 60/798,602, filed May 8, 2006; 60/801,687, filed May 19, 2006 and 60/889,958, filed Feb. 15, 2007. The entire contents of each of these applications are hereby incorporated by reference herein.

SUBMISSION OF SEQUENCE LISTING

The Sequence Listing associated with this application is filed in electronic format via EFS-Web and hereby incorporated by reference into the specification in its entirety. The name of the text file containing the Sequence Listing is Sequence_Listing_(—)32279_(—)00060. The size of the text file is 523 KB, and the text file was created on Jun. 3, 2013.

The present invention relates generally to the field of molecular biology and concerns a method for improving various plant growth characteristics by modulating expression in a plant of a nucleic acid encoding a GRP (Growth-Related Protein). The present invention also concerns plants having modulated expression of a nucleic acid encoding a GRP, which plants have improved growth characteristics relative to corresponding wild type plants or other control plants. The invention also provides constructs useful in the methods of the invention.

The ever-increasing world population and the dwindling supply of arable land available for agriculture fuels research towards increasing the efficiency of agriculture. Conventional means for crop and horticultural improvements utilise selective breeding techniques to identify plants having desirable characteristics. However, such selective breeding techniques have several drawbacks, namely that these techniques are typically labour intensive and result in plants that often contain heterogeneous genetic components that may not always result in the desirable trait being passed on from parent plants. Advances in molecular biology have allowed mankind to modify the germplasm of animals and plants. Genetic engineering of plants entails the isolation and manipulation of genetic material (typically in the form of DNA or RNA) and the subsequent introduction of that genetic material into a plant. Such technology has the capacity to deliver crops or plants having various improved economic, agronomic or horticultural traits.

A trait of particular economic interest is increased yield. Yield is normally defined as the measurable produce of economic value from a crop. This may be defined in terms of quantity and/or quality. Yield is directly dependent on several factors, for example, the number and size of the organs, plant architecture (for example, the number of branches), seed production, leaf senescence and more. Root development, nutrient uptake, stress tolerance and early vigour may also be important factors in determining yield. Optimizing the abovementioned factors may therefore contribute to increasing crop yield.

Seed yield is a particularly important trait, since the seeds of many plants are important for human and animal nutrition. Crops such as corn, rice, wheat, canola and soybean account for over half the total human caloric intake, whether through direct consumption of the seeds themselves or through consumption of meat products raised on processed seeds. They are also a source of sugars, oils and many kinds of metabolites used in industrial processes. Seeds contain an embryo (the source of new shoots and roots) and an endosperm (the source of nutrients for embryo growth during germination and during early growth of seedlings). The development of a seed involves many genes, and requires the transfer of metabolites from the roots, leaves and stems into the growing seed. The endosperm, in particular, assimilates the metabolic precursors of carbohydrates, oils and proteins and synthesizes them into storage macromolecules to fill out the grain.

Another important trait for many crops is early vigour. Improving early vigour is an important objective of modern rice breeding programs in both temperate and tropical rice cultivars. Long roots are important for proper soil anchorage in water-seeded rice. Where rice is sown directly into flooded fields, and where plants must emerge rapidly through water, longer shoots are associated with vigour. Where drill-seeding is practiced, longer mesocotyls and coleoptiles are important for good seedling emergence. The ability to engineer early vigour into plants would be of great importance in agriculture. For example, poor early vigor has been a limitation to the introduction of maize (Zea mays L.) hybrids based on Corn Belt germplasm in the European Atlantic.

A further important trait is that of improved abiotic stress tolerance. Abiotic stress is a primary cause of crop loss worldwide, reducing average yields for most major crop plants by more than 50% (Wang et al., Planta (2003) 218: 1-14). Abiotic stresses may be caused by drought, salinity, extremes of temperature, chemical toxicity and oxidative stress. The ability to improve plant tolerance to abiotic stress would be of great economic advantage to farmers worldwide and would allow for the cultivation of crops during adverse conditions and in territories where cultivation of crops may not otherwise be possible.

Crop yield may therefore be increased by optimising one of the above-mentioned factors.

Depending on the end use, the modification of certain yield traits may be favoured over others. For example for applications such as forage or wood production, or bio-fuel resource, an increase in the vegetative parts of a plant may be desirable, and for applications such as flour, starch or oil production, an increase in seed parameters may be particularly desirable. Even amongst the seed parameters, some may be favoured over others, depending on the application. Various mechanisms may contribute to increasing seed yield, whether that is in the form of increased seed size or increased seed number.

One approach to increasing yield (seed yield and/or biomass) in plants may be through modification of the inherent growth mechanisms of a plant, such as the cell cycle or various signalling pathways involved in plant growth or in defense mechanisms.

It has now been found that various growth characteristics may be improved in plants by modulating expression in a plant of a nucleic acid encoding a GRP (Growth-Related Protein) in a plant. The GRP may be one of the following: a MADS-box transcription factor (OsMADS15), a PLT transcription factor, a bHLH transcription factor, an SPL15 transcription factor, and a halotolerance protein (HAL3).

BACKGROUND Halotolerance Proteins

Many enzymatic processes in a cell require the involvement of Coenzyme A (CoA or CoASH). Coenzyme A (CoASH) itself is a highly polar molecule, consisting of adenosine 3′,5′-diphosphate linked to 4-phosphopantethenic acid (Vitamin B5) and thence to β-mercaptoethylamine. The free SH group may be esterified, depending on the process in which CoA is involved. The pathway of CoA synthesis has been elucidated in bacteria, animals and plants. In plants, the conversion of the CoA precursor 4′-phosphopantothenoyl-cysteine (PPC) into 4′-phosphopantetheine is catalysed by the flavoprotein 4′-phosphopantothenoyl-cysteine decarboxylase (PPCDC or HAL3, Kupke et al. J. Biol. Chem. 276, 19190-19196, 2001). The gene encoding HAL3 proteins may be part of a small gene family: the Arabidopsis genome comprises two isoforms (AtHAL3a and AtHAL3b; Espinoza-Ruiz et al. Plant J. 20, 529-539, 1999), in tobacco 3 HAL3 genes are present (Yonamine et al. J. Exp. Bot. 55, 387-395, 2004), though in rice HAL3 is a single copy gene. It is suggested that AtHAL3 and other HAL3 proteins function as a trimer, with each monomer having a flavin mononucleotide (FMN) bound (Albert et al. Structure 8, 961-969, 2000). The FMN cofactor is postulated to play a role in the redox reaction generating 4′-phosphopantetheine.

The molecular function of HAL3 proteins is not fully elucidated yet. The HAL3 proteins show homology to the yeast SIS2 protein, which is involved in halotolerance (Ferrando et al., Mol. Cell. Biol. 15, 5470-5481). Plants or plant cells ectopically expressing HAL3 show improved salt, osmotic or lithium stress tolerance (Espinoza-Ruiz et al., 1999; Yonamine et al., 2004). Tobacco HAL3a overexpression in BY2 cells reportedly caused an increase in intracellular proline content, which may contribute to the salt tolerant phenotype (Yonamine et al., 2004). Furthermore, Arabidopsis plants overexpressing AtHAL3a displayed a faster growth rate than the wild type plants (Espinoza-Ruiz et al., 1999). The AtHAL3b protein was shown to interact with the cell cycle protein CDKB1:1 (WO 00/36124), therefore it was postulated that AtHAL3b is useful for conferring salt stress tolerance to plants and for increasing the growth rate of plants under salt stress conditions Surprisingly, it has now been found that preferentially increasing expression of a nucleic acid encoding a HAL3 polypeptide in expanding tissues gives plants having increased yield relative to control plants, which yield increase is at least 10% compared to the control plants.

Transcription Factors

Transcription factors are usually defined as proteins that bind to a cis-regulatory element (eg. an enhancer, a TATA box) and that, in association with RNA polymerase, are capable of activating and/or repressing transcription. The Arabidopsis genome codes for at least 1533 transcriptional regulators, which account for ˜5.9% of its estimated total number of genes (Riechmann et al., 2000 (Science Vol. 290, 2105-2109)).

MADS15

The MADS-box genes constitute a large gene family of eukaryotic transcriptional regulators involved in diverse aspects of yeast, plant and animal development. MADS-box genes encode a strongly conserved MADS domain responsible for DNA binding to specific boxes in the regulatory region of their target genes. The gene family can be divided into two main lineages, type I and type II. Type II genes are also named MIKC-type proteins, referring to the four functional domains they possess (FIG. 5, (Jack, Plant Mol. Biol. 46, 515-520, 2001)):

-   -   MADS for DNA binding, about 60 amino acids (highly conserved)         located at the N-terminal end of the protein;     -   I for intervening domain (less conserved), involved in the         selective formation of MADS dimer;     -   K for keratin domain (well conserved) responsible for         dimerisation;     -   C for C-terminal region (variable in sequence and length)         involved in transcriptional activation, or in the formation of a         multimeric transcription factor complex.

Over 100 MADS-box genes have been identified in Arabidopsis, and have been phylogenetically classified into 12 clades, each clade having specific deviations from the MADS consensus (Thiessen et al. J. Mol. Evol. 43, 484-516, 1996). OsMADS15 belongs to the SQUA clade (for SQUAMOSA, from Antirrhinum majus). Genes of the SQUA clade are classified as A function organ identity genes with reference to the ABC floral organ identity specification model, proposed by Coen and Meyerowitz in 1991 (Nature 353, 31-7). Besides OsMADS15, rice OsMADS14, OsMADS18, and OsMADS20 are also part of the SQUA clade.

The SQUA clade in dicotyledonous plants (dicots) is subdivided into two subgroups, the AP1 and the FUL subclades (in which OsMADS15 clusters). These subclades diverge essentially with respect to the specific amino acid motifs located at the C-terminus of their respective proteins (Litt and Irish, Genetics 165, 821-833, 2003). In addition to the presence of a specific AP1 amino acid motif, the dicot AP1 clade related proteins usually comprise a farnesylation motif at their C-terminus (this motif is CAAX, where C is cysteine, A is usually an aliphatic amino acid, and X is methionine, glutamine, serine, cysteine or alanine). In monocotyledonous plants (monocots), the SQUA clade proteins are also subdivided into two main groups, which may be distinguished based on conserved C-terminal motifs located within the last 15 amino acids of the proteins: LPPWMLS (for example OsMADS15, SEQ ID NO: 117) and LPPWMLR (for example OsMADS18). In contrast to dicot sequences of the SQUA clade, monocot sequences of the SQUA clade do not possess a farnesylation motif at their C-terminus.

OsMADS15 was postulated to function in a complex with other proteins to control organ formation. However, so far no mutants with a visible phenotype have been identified; no experimental data have been presented relating to ectopic expression or down-regulated expression of OsMADS15, except for the data presented in WO 01/14559 (EP1209232, U.S. Pat. No. 6,995,302). In this disclosure, transgenic Fagopyrum esculentum plants expressing OsMADS15 in sense direction showed increased branching, whereas transgenics expressing the antisense construct had decreased growth and suppressed branching. Kalanchoë daigremontiana transformed with the sense construct had leaf development around the roots, which was taken as an indication of increased branching. The authors stated that no changes were observed in terms of flower development and structure of these flowers. The orthologue of OsMADS15 in Arabidopsis is APETALA1 (AP1). Ectopic expression of AP1 results in a decrease of flowering time, and AP1 mutants exhibit delayed flowering and have abnormal flowers.

PLT

The AP2(apetala2)/ERF (ethylene-responsive responsive element-binding factor) family comprises transcription factors with at least one highly conserved DNA binding domain, the AP2 domain. The AP2 domain was originally described in APETALA2 (AP2), an Arabidopsis protein involved in developmental programs such as meristem identity regulation and floral organ specification (Jofuku et al., (1994) Plant Cell 6, 1211-1225). AP2/ERF proteins are divided into subfamilies based on whether they contain one (ERF subfamily) or two (AP2 subfamily) DNA binding domains (FIG. 12). More than 140 AP2/ERF genes have been identified in the Arabidopsis thaliana genome (Reichmann et al. (2000) Science 290: 2105-2110), amongst which up to 18 belong to the AP2 subfamily (Kim et al. (2006) Mol Bio Evol 23(1): 107-120).

Two Arabidopsis AP2 subfamily transcription factor polypeptides, encoded by the Plethora 1 (PLT1) and Plethora 2 (PLT2) genes, collectively called PLT genes, have been shown to be required for stem cell specification and maintenance specifically in the root meristem. In RT-PCR analysis, PLT transcripts were mainly detected in roots, indicating that PLT expression is strongly associated with root identity. Ectopic PLT expression in the Arabidopsis embryo induces homeotic transformation of apical domains into root stem cells, roots, or hypocotyls (Aida et al (2004) Cell 119:109-120).

US patent application 2004/0045049 and international patent application WO03/013227 provide the nucleic acid sequence encoding the Arabidopsis PLT1 transcription factor (referred to in the applications as G1793). Overexpression of G1793 (using the CaMV 35S promoter) in Arabidopsis was reported to produce alterations in cotyledon morphology, a mild reduction in overall plant size and thin inflorescences (possibly with abnormal flowers) compared to wild type controls. G1793 overexpressors produced more seed oil than control plants. Nucleic acid sequences encoding potential Glycine max, Oryza sativa and Zea mays orthologs are provided.

International patent application WO 03/002751 provides for a Glycine max nucleic acid sequence encoding a PLT polypeptide, with sequence similarity to a corn nucleic acid sequence identified by gene profiling (by DNA microarray).

International patent application WO 05/075655 provides for Oryza sativa and Zea mays nucleic acid sequences with sequence similarity to the Arabidopsis PLT genes.

bHLH

The basic/helix-loop-helix (bHLH) proteins are a superfamily of transcription factors that bind as dimers to specific DNA target sites and that have been well characterized in non-plant eukaryotes as important regulatory components in diverse biological processes. The distinguishing characteristic of the bHLH family is a bipartite domain consisting of approximately 60 amino acids. This bipartite domain is comprised of a DNA-binding basic region, which binds to a consensus hexanucleotide E-box and two α-helices separated by a variable loop region. The two α-helices promote dimerization, allowing the formation of homo- and heterodimers between different family members. While the bHLH domain is evolutionarily conserved, there is little sequence similarity between clades beyond the domain.

Bailey et al., 2003 (The Plant Cell, Vol. 15, 2497-2501) report the total number of detected bHLH genes in Arabidopsis thaliana to be 162, making bHLH genes one of the largest families of transcription factors in Arabidopsis; the rice genome reportedly contains 131 bHLH genes (Buck and Atchley, 2003 (J. Mol. Evol. 56:742-750)). Heim et al., 2003 (Mol. Biol. Evol. 20(5):735-747) identified 12 subfamilies of bHLH genes from Arabidopsis thaliana based on structural similarities.

The bHLH proteins from plants that have been characterized have been reported to function in anthocyanin biosynthesis, phytochrome signaling, globulin expression, fruit dehiscence, carpel and epidermal development (Buck and Atchley, 2003).

SPL

The Squamosa Qromoter binding protein-like (SPL) transcription factor polypeptides are structurally diverse proteins that share a highly conserved DNA binding domain (DBD) of about 80 amino acid residues in length (Klein et al. (1996) Mol Gen Genet. 259: 7-16; Cardon et al. (1999) Gene 237: 91-104). The SPL transcription factor DNA consensus sequence binding site in the promoter of target genes is 5′-TNCGTACAA-3′ where N represents any base. Within the SPL DBD are ten conserved cysteine (Cys) or histidine (His) residues (see FIG. 23) of which eight are zinc coordinating residues binding two zinc ions necessary for the formation of SPL specific zinc finger tertiary structure (Yamasaki et al. (2004) J Mol Biol 337: 49-63). A second conserved feature within the SPL DBD is a bipartite nuclear localisation signal. Outside of the DBD, a micro RNA (miRNA) target motif (miR156) is found in most of the nucleic acid sequences encoding SPL transcription factor polypeptides (either in the coding region, or the 3′ UTR) across the plant kingdom (Rhoades et al. (2002) Cell 110: 513-520). miRNAs control SPL gene expression post-transcriptionally by targeting SPL encoding mRNAs for degradation or by translational repression.

Riechmann et al. (Science 290: 2105-2109, 2000) report 16 SPL transcription factor polypeptides in Arabidopsis thaliana, with little sequence similarity between themselves (apart from the abovementioned features), the size of the deduced SPL polypeptide ranging from 131 to 927 amino acids. Nevertheless, pairs of SPL transcription factor polypeptides sharing higher sequence homology were detected within the SPL family of this plant (Cardon et al. (1999)).

The SPL transcription factor polypeptides (only found in plants) characterized to date have been shown to function in plant development, in particular in flower development. Transgenic plants overexpressing an SPL3 transcription factor polypeptide were reported to flower earlier (Cardon et al. (1997) Plant J 12: 367-377).

In European patent application EP1033405, the nucleic acid and deduced polypeptide sequences of the SPL15 transcription factor polypeptide are presented.

In international patent application WO03013227, a nucleic acid sequence (and deduced polypeptide sequence; internal reference G2346) is presented that encodes part of the SPL15 transcription factor polypeptide however 38 amino acids from the C-terminal end of the SPL15 transcription factor. Transgenic Arabidopsis thaliana plants constitutively overexpressing the modified SPL15 transcription factor (or G2346) polypeptide have slightly enlarged cotyledons. At later stages of development, the same plants are reported to show no consistent differences from control plants.

SUMMARY OF THE INVENTION

Surprisingly, it has now been found that preferentially increasing expression of a nucleic acid encoding a HAL3 polypeptide in expanding tissues gives plants having enhanced yield-related traits, in particular increased early vigour and increased seed yield relative to control plants, which seed yield increase is at least 10% compared to the control plants.

According to another embodiment of present invention, there is provided a method for enhancing yield-related traits, in particular for increasing early vigour of a plant and increasing seed yield of a plant, relative to control plants, comprising preferentially increasing expression of a nucleic acid encoding a HAL3 polypeptide in expanding tissues of a plant.

Surprisingly, it has now been found that modulating expression of a nucleic acid encoding a MADS15 polypeptide gives plants having enhanced yield-related traits, in particular increased yield relative to control plants.

According one embodiment, there is provided a method for increasing plant yield relative to control plants, comprising increasing expression of a nucleic acid encoding a MADS15 polypeptide in a plant. The increased yield comprised increased vegetative biomass but not increased seed yield.

According to another embodiment, the present invention provides methods for increasing yield of a plant relative to control plants, comprising decreasing the level and/or activity of an endogenous MADS15 polypeptide. The increased yield comprised higher seed yield, but did not comprise increased vegetative biomass.

Surprisingly, it has now been found that increasing expression of a nucleic acid encoding a PLT transcription factor polypeptide gives plants having enhanced yield related traits, in particular increased yield relative to control plants.

According to a further embodiment, there is provided a method for increasing plant yield relative to control plants, comprising increasing expression in a plant of a nucleic acid encoding a PLT transcription factor polypeptide.

Surprisingly, it has now been found that modulating expression in a plant of a nucleic acid encoding a particular class of bHLH transcription factor gives plants having enhanced yield-related traits relative to control plants. The particular class of bHLH transcription factor suitable for enhancing yield-related traits in plants is described in detail below.

According to a further embodiment, the present invention provides a method for enhancing yield-related traits in plants relative to control plants, comprising modulating expression in a plant of a nucleic acid encoding a particular class of bHLH transcription factor.

Surprisingly, it has now been found that increasing expression in a plant of a nucleic acid encoding an SPL15 transcription factor polypeptide gives plants having enhanced yield related traits, in particular increased yield relative to control plants.

According to a further embodiment, the invention provides a method for increasing yield in plants relative to control plants, comprising increasing expression in a plant of a nucleic acid encoding an SPL15 transcription factor polypeptide.

DEFINITIONS Polypeptide(s)/Protein(s)

The terms “polypeptide” and “protein” are used interchangeably herein and refer to amino acids in a polymeric form of any length.

Polynucleotide(s)/Nucleic Acid(s)/Nucleic Acid Sequence(s)/Nucleotide Sequence(s)

The terms “polynucleotide(s)”, “nucleic acid sequence(s)”, “nucleotide sequence(s)”, “nucleic acid(s)” are used interchangeably herein and refer to nucleotides, either ribonucleotides or deoxyribonucleotides or a combination of both, in a polymeric form of any length.

Control Plant(s)

The choice of suitable control plants is a routine part of an experimental setup and may include corresponding wild type plants or corresponding plants without the gene of interest. The control plant is typically of the same plant species or even of the same variety as the plant to be assessed. The control plant may also be a nullizygote of the plant to be assessed. A “control plant” as used herein refers not only to whole plants, but also to plant parts, including seeds and seed parts.

Homoloque(s)

“Homologues” of a protein encompass peptides, oligopeptides, polypeptides, proteins and enzymes having amino acid substitutions, deletions and/or insertions relative to the unmodified protein in question and having similar biological and functional activity as the unmodified protein from which they are derived.

A deletion refers to removal of one or more amino acids from a protein.

An insertion refers to one or more amino acid residues being introduced into a predetermined site in a protein. Insertions may comprise N-terminal and/or C-terminal fusions as well as intra-sequence insertions of single or multiple amino acids. Generally, insertions within the amino acid sequence will be smaller than N- or C-terminal fusions, of the order of about 1 to 10 residues. Examples of N- or C-terminal fusion proteins or peptides include the binding domain or activation domain of a transcriptional activator as used in the yeast two-hybrid system, phage coat proteins, (histidine)-6-tag, glutathione S-transferase-tag, protein A, maltose-binding protein, dihydrofolate reductase, Tag·100 epitope, c-myc epitope, FLAG®-epitope, lacZ, CMP (calmodulin-binding peptide), HA epitope, protein C epitope and VSV epitope.

A substitution refers to replacement of amino acids of the protein with other amino acids having similar properties (such as similar hydrophobicity, hydrophilicity, antigenicity, propensity to form or break α-helical structures or β-sheet structures). Amino acid substitutions are typically of single residues, but may be clustered depending upon functional constraints placed upon the polypeptide; insertions will usually be of the order of about 1 to 10 amino acid residues. The amino acid substitutions are preferably conservative amino acid substitutions. Conservative substitution tables are well known in the art (see for example Creighton (1984) Proteins. W.H. Freeman and Company and Table 1 below).

TABLE 1 Examples of conserved amino acid substitutions Conservative Conservative Residue Substitutions Residue Substitutions Ala Ser Leu Ile; Val Arg Lys Lys Arg; Gln Asn Gln; His Met Leu; Ile Asp Glu Phe Met; Leu; Tyr Gln Asn Ser Thr; Gly Cys Ser Thr Ser; Val Glu Asp Trp Tyr Gly Pro Tyr Trp; Phe His Asn; Gln Val Ile; Leu Ile Leu, Val

Amino acid substitutions, deletions and/or insertions may readily be made using peptide synthetic techniques well known in the art, such as solid phase peptide synthesis and the like, or by recombinant DNA manipulation. Methods for the manipulation of DNA sequences to produce substitution, insertion or deletion variants of a protein are well known in the art. For example, techniques for making substitution mutations at predetermined sites in DNA are well known to those skilled in the art and include M13 mutagenesis, T7-Gen in vitro mutagenesis (USB, Cleveland, Ohio), QuickChange Site Directed mutagenesis (Stratagene, San Diego, Calif.), PCR-mediated site-directed mutagenesis or other site-directed mutagenesis protocols.

Derivatives

“Derivatives” include peptides, oligopeptides, polypeptides which may, compared to the amino acid sequence of the naturally-occurring form of the protein, such as the protein of interest, comprise substitutions of amino acids with non-naturally occurring amino acid residues, or additions of non-naturally occurring amino acid residues. “Derivatives” of a protein also encompass peptides, oligopeptides, polypeptides which comprise naturally occurring altered (glycosylated, acylated, prenylated, phosphorylated, myristoylated, sulphated etc.) or non-naturally altered amino acid residues compared to the amino acid sequence of a naturally-occurring form of the polypeptide. A derivative may also comprise one or more non-amino acid substituents or additions compared to the amino acid sequence from which it is derived, for example a reporter molecule or other ligand, covalently or non-covalently bound to the amino acid sequence, such as a reporter molecule which is bound to facilitate its detection, and non-naturally occurring amino acid residues relative to the amino acid sequence of a naturally-occurring protein.

Ortholoque(s)/Paraloque(s)

Orthologues and paralogues encompass evolutionary concepts used to describe the ancestral relationships of genes. Paralogues are genes within the same species that have originated through duplication of an ancestral gene and orthologues are genes from different organisms that have originated through speculation.

Domain

The term “domain” refers to a set of amino acids conserved at specific positions along an alignment of sequences of evolutionarily related proteins. While amino acids at other positions can vary between homologues, amino acids that are highly conserved at specific positions indicate amino acids that are likely essential in the structure, stability or function of a protein. Identified by their high degree of conservation in aligned sequences of a family of protein homologues, they can be used as identifiers to determine if any polypeptide in question belongs to a previously identified polypeptide family.

Motif/Consensus Sequence/Signature

The term “motif” or “consensus sequence” or “signature” refers to a short conserved region in the sequence of evolutionarily related proteins. Motifs are frequently highly conserved parts of domains, but may also include only part of the domain, or be located outside of conserved domain (if all of the amino acids of the motif fall outside of a defined domain).

Hybridisation

The term “hybridisation” as defined herein is a process wherein substantially homologous complementary nucleotide sequences anneal to each other. The hybridisation process can occur entirely in solution, i.e. both complementary nucleic acids are in solution. The hybridisation process can also occur with one of the complementary nucleic acids immobilised to a matrix such as magnetic beads, Sepharose beads or any other resin. The hybridisation process can furthermore occur with one of the complementary nucleic acids immobilised to a solid support such as a nitro-cellulose or nylon membrane or immobilised by e.g. photolithography to, for example, a siliceous glass support (the latter known as nucleic acid arrays or microarrays or as nucleic acid chips). In order to allow hybridisation to occur, the nucleic acid molecules are generally thermally or chemically denatured to melt a double strand into two single strands and/or to remove hairpins or other secondary structures from single stranded nucleic acids.

The term “stringency” refers to the conditions under which a hybridisation takes place. The stringency of hybridisation is influenced by conditions such as temperature, salt concentration, ionic strength and hybridisation buffer composition. Generally, low stringency conditions are selected to be about 30° C. lower than the thermal melting point (T_(m)) for the specific sequence at a defined ionic strength and pH. Medium stringency conditions are when the temperature is 20° C. below T_(m), and high stringency conditions are when the temperature is 10° C. below T_(m). High stringency hybridisation conditions are typically used for isolating hybridising sequences that have high sequence similarity to the target nucleic acid sequence. However, nucleic acids may deviate in sequence and still encode a substantially identical polypeptide, due to the degeneracy of the genetic code. Therefore medium stringency hybridisation conditions may sometimes be needed to identify such nucleic acid molecules.

The T_(m) is the temperature under defined ionic strength and pH, at which 50% of the target sequence hybridises to a perfectly matched probe. The T_(m) is dependent upon the solution conditions and the base composition and length of the probe. For example, longer sequences hybridise specifically at higher temperatures. The maximum rate of hybridisation is obtained from about 16° C. up to 32° C. below T_(m). The presence of monovalent cations in the hybridisation solution reduce the electrostatic repulsion between the two nucleic acid strands thereby promoting hybrid formation; this effect is visible for sodium concentrations of up to 0.4M (for higher concentrations, this effect may be ignored). Formamide reduces the melting temperature of DNA-DNA and DNA-RNA duplexes with 0.6 to 0.7° C. for each percent formamide, and addition of 50% formamide allows hybridisation to be performed at 30 to 45° C., though the rate of hybridisation will be lowered. Base pair mismatches reduce the hybridisation rate and the thermal stability of the duplexes. On average and for large probes, the T_(m) decreases about 1° C. per % base mismatch. The T_(m) may be calculated using the following equations, depending on the types of hybrids:

1) DNA-DNA hybrids (Meinkoth and Wahl, Anal. Biochem., 138: 267-284, 1984):

T _(m)=81.5° C.+16.6×log₁₀[Na⁺]^(a)+0.41×%[G/C ^(b)]−500×[L ^(c)]⁻¹−0.61×% formamide

2) DNA-RNA or RNA-RNA hybrids:

T _(m)=79.8+18.5 (log₁₀[Na⁺]^(a))+0.58 (% G/C ^(b))+11.8 (% G/C ^(b))²−820/L ^(c)

3) oligo-DNA or oligo-RNA^(d) hybrids: For <20 nucleotides: T_(m)=2 (l_(n)) For 20-35 nucleotides: T_(m)=22+1.46 (l_(n))

^(a) or for other monovalent cation, but only accurate in the 0.01-0.4 M range.

^(b) only accurate for % GC in the 30% to 75% range.

^(c) L=length of duplex in base pairs.

^(d) Oligo, oligonucleotide; l_(n), effective length of primer=2×(no. of G/C)+(no. of A/T).

Non-specific binding may be controlled using any one of a number of known techniques such as, for example, blocking the membrane with protein containing solutions, additions of heterologous RNA, DNA, and SDS to the hybridisation buffer, and treatment with Rnase. For non-homologous probes, a series of hybridizations may be performed by varying one of (i) progressively lowering the annealing temperature (for example from 68° C. to 42° C.) or (ii) progressively lowering the formamide concentration (for example from 50% to 0%). The skilled artisan is aware of various parameters which may be altered during hybridisation and which will either maintain or change the stringency conditions.

Besides the hybridisation conditions, specificity of hybridisation typically also depends on the function of post-hybridisation washes. To remove background resulting from non-specific hybridisation, samples are washed with dilute salt solutions. Critical factors of such washes include the ionic strength and temperature of the final wash solution: the lower the salt concentration and the higher the wash temperature, the higher the stringency of the wash. Wash conditions are typically performed at or below hybridisation stringency. A positive hybridisation gives a signal that is at least twice of that of the background. Generally, suitable stringent conditions for nucleic acid hybridisation assays or gene amplification detection procedures are as set forth above. More or less stringent conditions may also be selected. The skilled artisan is aware of various parameters which may be altered during washing and which will either maintain or change the stringency conditions.

For example, typical high stringency hybridisation conditions for DNA hybrids longer than 50 nucleotides encompass hybridisation at 65° C. in 1×SSC or at 42° C. in 1×SSC and 50% formamide, followed by washing at 65° C. in 0.3×SSC. Examples of medium stringency hybridisation conditions for DNA hybrids longer than 50 nucleotides encompass hybridisation at 50° C. in 4×SSC or at 40° C. in 6×SSC and 50% formamide, followed by washing at 50° C. in 2×SSC. The length of the hybrid is the anticipated length for the hybridising nucleic acid. When nucleic acids of known sequence are hybridised, the hybrid length may be determined by aligning the sequences and identifying the conserved regions described herein. 1×SSC is 0.15M NaCl and 15 mM sodium citrate; the hybridisation solution and wash solutions may additionally include 5×Denhardt's reagent, 0.5-1.0% SDS, 100 μg/ml denatured, fragmented salmon sperm DNA, 0.5% sodium pyrophosphate.

For the purposes of defining the level of stringency, reference can be made to Sambrook et al. (2001) Molecular Cloning: a laboratory manual, 3rd Edition Cold Spring Harbor Laboratory Press, CSH, New York or to Current Protocols in Molecular Biology, John Wiley & Sons, N.Y. (1989 and yearly updates).

Splice Variant

The term “splice variant” as used herein encompasses variants of a nucleic acid sequence in which selected introns and/or exons have been excised, replaced, displaced or added, or in which introns have been shortened or lengthened. Such variants will be ones in which the biological activity of the protein is substantially retained; this may be achieved by selectively retaining functional segments of the protein. Such splice variants may be found in nature or may be manmade. Methods for predicting and isolating such splice variants are well known in the art (see for example Foissac and Schiex, BMC Bioinformatics. 2005; 6: 25).

Allelic Variant

Alleles or allelic variants are alternative forms of a given gene, located at the same chromosomal position. Allelic variants encompass Single Nucleotide Polymorphisms (SNPs), as well as Small Insertion/Deletion Polymorphisms (INDELs). The size of INDELs is usually less than 100 bp. SNPs and INDELs form the largest set of sequence variants in naturally occurring polymorphic strains of most organisms.

Gene Shuffling/Directed Evolution

Gene shuffling or directed evolution consists of iterations of DNA shuffling followed by appropriate screening and/or selection to generate variants of nucleic acids or portions thereof encoding proteins having a modified biological activity (Castle et al., (2004) Science 304(5674): 1151-4; U.S. Pat. Nos. 5,811,238 and 6,395,547).

Regulatory Element/Control Sequence/Promoter

The terms “regulatory element”, “control sequence” and “promoter” are all used interchangeably herein and are to be taken in a broad context to refer to regulatory nucleic acid sequences capable of effecting expression of the sequences to which they are ligated. The term “promoter” typically refers to a nucleic acid control sequence located upstream from the transcriptional start of a gene and which is involved in recognising and binding of RNA polymerase and other proteins, thereby directing transcription of an operably linked nucleic acid. Encompassed by the aforementioned terms are transcriptional regulatory sequences derived from a classical eukaryotic genomic gene (including the TATA box which is required for accurate transcription initiation, with or without a CCAAT box sequence) and additional regulatory elements (i.e. upstream activating sequences, enhancers and silencers) which alter gene expression in response to developmental and/or external stimuli, or in a tissue-specific manner. Also included within the term is a transcriptional regulatory sequence of a classical prokaryotic gene, in which case it may include a −35 box sequence and/or −10 box transcriptional regulatory sequences. The term “regulatory element” also encompasses a synthetic fusion molecule or derivative that confers, activates or enhances expression of a nucleic acid molecule in a cell, tissue or organ.

A “plant promoter” comprises regulatory elements, which mediate the expression of a coding sequence segment in plant cells. Accordingly, a plant promoter need not be of plant origin, but may originate from viruses or micro-organisms, for example from viruses which attack plant cells. The “plant promoter” can also originate from a plant cell, e.g. from the plant which is transformed with the nucleic acid sequence to be expressed in the inventive process and described herein. This also applies to other “plant” regulatory signals, such as “plant” terminators. The promoters upstream of the nucleotide sequences useful in the methods of the present invention can be modified by one or more nucleotide substitution(s), insertion(s) and/or deletion(s) without interfering with the functionality or activity of either the promoters, the open reading frame (ORF) or the 3′-regulatory region such as terminators or other 3′ regulatory regions which are located away from the ORF. It is furthermore possible that the activity of the promoters is increased by modification of their sequence, or that they are replaced completely by more active promoters, even promoters from heterologous organisms. For expression in plants, the nucleic acid molecule must, as described above, be linked operably to or comprise a suitable promoter which expresses the gene at the right point in time and with the required spatial expression pattern.

For the identification of functionally equivalent promoters, the promoter strength and/or expression pattern of a candidate promoter may be analysed for example by operably linking the promoter to a reporter gene and assaying the expression level and pattern of the reporter gene in various tissues of the plant. Suitable well-known reporter genes include for example beta-glucuronidase or beta galactosidase. The promoter activity is assayed by measuring the enzymatic activity of the beta-glucuronidase or beta-galactosidase. The promoter strength and/or expression pattern may then be compared to that of a reference promoter (such as the one used in the methods of the present invention). Alternatively, promoter strength may be assayed by quantifying mRNA levels or by comparing mRNA levels of the nucleic acid used in the methods of the present invention, with mRNA levels of housekeeping genes such as 18S rRNA, using methods known in the art, such as Northern blotting with densitometric analysis of autoradiograms, quantitative real-time PCR or RT-PCR (Heid et al., 1996 Genome Methods 6: 986-994). Generally by “weak promoter” is intended a promoter that drives expression of a coding sequence at a low level. By “low level” is intended at levels of about 1/10,000 transcripts to about 1/100,000 transcripts, to about 1/500,0000 transcripts per cell. Conversely, a “strong promoter” drives expression of a coding sequence at high level, or at about 1/10 transcripts to about 1/100 transcripts to about 1/1,000 transcripts per cell.

Operably Linked

The term “operably linked” as used herein refers to a functional linkage between the promoter sequence and the gene of interest, such that the promoter sequence is able to initiate transcription of the gene of interest.

Constitutive Promoter

A “constitutive promoter” refers to a promoter that is transcriptionally active during most, but not necessarily all, phases of growth and development and under most environmental conditions, in at least one cell, tissue or organ. Table 2 below gives examples of constitutive promoters.

TABLE 2 Examples of constitutive promoters Gene Source Reference Actin McElroy et al, Plant Cell, 2: 163-171, 1990 HMGB WO 2004/070039 CAMV 35S Odell et al, Nature, 313: 810-812, 1985 CaMV 19S Nilsson et al., Physiol. Plant. 100: 456-462, 1997 GOS2 de Pater et al, Plant J Nov; 2(6): 837-44, 1992, WO 2004/065596 Ubiquitin Christensen et al, Plant Mol. Biol. 18: 675-689, 1992 Rice cyclophilin Buchholz et al, Plant Mol Biol. 25(5): 837-43, 1994 Maize H3 histone Lepetit et al, Mol. Gen. Genet. 231: 276-285, 1992 Alfalfa H3 Wu et al. Plant Mol. Biol. 11: 641-649, 1988 histone Actin 2 An et al, Plant J. 10(1); 107-121, 1996 34S FMV Sanger et al., Plant. Mol. Biol., 14, 1990: 433-443 Rubisco U.S. Pat. No. 4,962,028 small subunit OCS Leisner (1988) Proc Natl Acad Sci USA 85(5): 2553 SAD1 Jain et al., Crop Science, 39 (6), 1999: 1696 SAD2 Jain et al., Crop Science, 39 (6), 1999: 1696 nos Shaw et al. (1984) Nucleic Acids Res. 12(20): 7831-7846 V-ATPase WO 01/14572 Super promoter WO 95/14098 G-box proteins WO 94/12015

Ubiquitous Promoter

A ubiquitous promoter is active in substantially all tissues or cells of an organism.

Developmentally-Regulated Promoter

A developmentally-regulated promoter is active during certain developmental stages or in parts of the plant that undergo developmental changes.

Inducible Promoter

An inducible promoter has induced or increased transcription initiation in response to a chemical (for a review see Gatz 1997, Annu. Rev. Plant Physiol. Plant Mol. Biol., 48:89-108), environmental or physical stimulus, or may be “stress-inducible”, i.e. activated when a plant is exposed to various stress conditions, or a “pathogen-inducible” i.e. activated when a plant is exposed to exposure to various pathogens.

Organ-Specific/Tissue-Specific Promoter

An organ-specific or tissue-specific promoter is one that is capable of preferentially initiating transcription in certain organs or tissues, such as the leaves, roots, seed tissue etc. For example, a “root-specific promoter” is a promoter that is transcriptionally active predominantly in plant roots, substantially to the exclusion of any other parts of a plant, whilst still allowing for any leaky expression in these other plant parts. Promoters able to initiate transcription in certain cells only are referred to herein as “cell-specific”.

A green tissue-specific promoter as defined herein is a promoter that is transcriptionally active predominantly in green tissue, substantially to the exclusion of any other parts of a plant, whilst still allowing for any leaky expression in these other plant parts.

Examples of green tissue-specific promoters which may be used to perform the methods of the invention are shown in Table 3 below.

TABLE 3 Examples of green tissue-specific promoters Gene Expression Reference Maize Orthophosphate dikinase Leaf specific Fukavama et al., 2001 Maize Phosphoenolpyruvate Leaf specific Kausch et al., 2001 carboxylase Rice Phosphoenolpyruvate Leaf specific Liu et al., 2003 carboxylase Rice small subunit Rubisco Leaf specific Nomura et al., 2000 rice beta expansin EXBP9 Shoot specific WO 2004/070039 Pigeonpea small subunit Leaf specific Panguluri et al., 2005 Rubisco Pea RBCS3A Leaf specific

Another example of a tissue-specific promoter is a meristem-specific promoter, which is transcriptionally active predominantly in meristematic tissue, substantially to the exclusion of any other parts of a plant, whilst still allowing for any leaky expression in these other plant parts

Terminator

The term “terminator” encompasses a control sequence which is a DNA sequence at the end of a transcriptional unit which signals 3′ processing and polyadenylation of a primary transcript and termination of transcription. The terminator can be derived from the natural gene, from a variety of other plant genes, or from T-DNA. The terminator to be added may be derived from, for example, the nopaline synthase or octopine synthase genes, or alternatively from another plant gene, or less preferably from any other eukaryotic gene.

Modulation

The term “modulation” means in relation to expression or gene expression, a process in which the expression level is changed by said gene expression in comparison to the control plant, preferably the expression level is increased. The original, unmodulated expression may be of any kind of expression of a structural RNA (rRNA, tRNA) or mRNA with subsequent translation. The term “modulating the activity” shall mean any change of the expression of the inventive nucleic acid sequences or encoded proteins, which leads to increased yield and/or increased growth of the plants.

Increased Expression/Overexpression

The term “increased expression” or “overexpression” as used herein means any form of expression that is additional to the original wild-type expression level.

Methods for increasing expression of genes or gene products are well documented in the art and include, for example, overexpression driven by appropriate promoters, the use of transcription enhancers or translation enhancers. Isolated nucleic acids which serve as promoter or enhancer elements may be introduced in an appropriate position (typically upstream) of a non-heterologous form of a polynucleotide so as to upregulate expression of a nucleic acid encoding the polypeptide of interest. For example, endogenous promoters may be altered in vivo by mutation, deletion, and/or substitution (see, Kmiec, U.S. Pat. No. 5,565,350; Zarling et al., PCT/US93/03868), or isolated promoters may be introduced into a plant cell in the proper orientation and distance from a gene of the present invention so as to control the expression of the gene.

If polypeptide expression is desired, it is generally desirable to include a polyadenylation region at the 3′-end of a polynucleotide coding region. The polyadenylation region can be derived from the natural gene, from a variety of other plant genes, or from T-DNA. The 3′ end sequence to be added may be derived from, for example, the nopaline synthase or octopine synthase genes, or alternatively from another plant gene, or less preferably from any other eukaryotic gene.

An intron sequence may also be added to the 5′ untranslated region (UTR) or the coding sequence of the partial coding sequence to increase the amount of the mature message that accumulates in the cytosol. Inclusion of a spliceable intron in the transcription unit in both plant and animal expression constructs has been shown to increase gene expression at both the mRNA and protein levels up to 1000-fold (Buchman and Berg (1988) Mol. Cell. biol. 8: 4395-4405; Callis et al. (1987) Genes Dev 1:1183-1200). Such intron enhancement of gene expression is typically greatest when placed near the 5′ end of the transcription unit. Use of the maize introns Adh1-S intron 1, 2, and 6, the Bronze-1 intron are known in the art. For general information see: The Maize Handbook, Chapter 116, Freeling and Walbot, Eds., Springer, N.Y. (1994).

Endogenous Gene

Reference herein to an “endogenous” gene not only refers to the gene in question as found in a plant in its natural form (i.e., without there being any human intervention), but also refers to that same gene (or a substantially homologous nucleic acid/gene) in an isolated form subsequently (re)introduced into a plant (a transgene). For example, a transgenic plant containing such a transgene may encounter a substantial reduction of the transgene expression and/or substantial reduction of expression of the endogenous gene.

Decreased Expression

Reference herein to “reduction or substantial elimination” is taken to mean a decrease in endogenous gene expression and/or polypeptide levels and/or polypeptide activity relative to control plants. The reduction or substantial elimination is in increasing order of preference at least 10%, 20%, 30%, 40% or 50%, 60%, 70%, 80%, 85%, 90%, or 95%, 96%, 97%, 98%, 99% or more reduced compared to that of control plants.

For the reduction or substantial elimination of expression an endogenous gene in a plant, a sufficient length of substantially contiguous nucleotides of a nucleic acid sequence is required. In order to perform gene silencing, this may be as little as 20, 19, 18, 17, 16, 15, 14, 13, 12, 11, 10 or fewer nucleotides, alternatively this may be as much as the entire gene (including the 5′ and/or 3′ UTR, either in part or in whole). The stretch of substantially contiguous nucleotides may be derived from the nucleic acid encoding the protein of interest (target gene), or from any nucleic acid capable of encoding an orthologue, paralogue or homologue of the protein of interest. Preferably, the stretch of substantially contiguous nucleotides is capable of forming hydrogen bonds with the target gene (either sense or antisense strand), more preferably, the stretch of substantially contiguous nucleotides has, in increasing order of preference, 50%, 60%, 70%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, 100% sequence identity to the target gene (either sense or antisense strand). A nucleic acid sequence encoding a (functional) polypeptide is not a requirement for the various methods discussed herein for the reduction or substantial elimination of expression of an endogenous gene.

This reduction or substantial elimination of expression may be achieved using routine tools and techniques. A preferred method for the reduction or substantial elimination of endogenous gene expression is by introducing and expressing in a plant a genetic construct into which the nucleic acid (in this case a stretch of substantially contiguous nucleotides derived from the gene of interest, or from any nucleic acid capable of encoding an orthologue, paralogue or homologue of any one of the protein of interest) is cloned as an inverted repeat (in part or completely), separated by a spacer (non-coding DNA).

In such a preferred method, expression of the endogenous gene is reduced or substantially eliminated through RNA-mediated silencing using an inverted repeat of a nucleic acid or a part thereof (in this case a stretch of substantially contiguous nucleotides derived from the gene of interest, or from any nucleic acid capable of encoding an orthologue, paralogue or homologue of the protein of interest), preferably capable of forming a hairpin structure. The inverted repeat is cloned in an expression vector comprising control sequences. A non-coding DNA nucleic acid sequence (a spacer, for example a matrix attachment region fragment (MAR), an intron, a polylinker, etc.) is located between the two inverted nucleic acids forming the inverted repeat. After transcription of the inverted repeat, a chimeric RNA with a self-complementary structure is formed (partial or complete). This double-stranded RNA structure is referred to as the hairpin RNA (hpRNA). The hpRNA is processed by the plant into siRNAs that are incorporated into an RNA-induced silencing complex (RISC). The RISC further cleaves the mRNA transcripts, thereby substantially reducing the number of mRNA transcripts to be translated into polypeptides. For further general details see for example, Grierson et al. (1998) WO 98/53083; Waterhouse et al. (1999) WO 99/53050).

Performance of the methods of the invention does not rely on introducing and expressing in a plant a genetic construct into which the nucleic acid is cloned as an inverted repeat, but any one or more of several well-known “gene silencing” methods may be used to achieve the same effects.

One such method for the reduction of endogenous gene expression is RNA-mediated silencing of gene expression (downregulation). Silencing in this case is triggered in a plant by a double stranded RNA sequence (dsRNA) that is substantially similar to the target endogenous gene. This dsRNA is further processed by the plant into about 20 to about 26 nucleotides called short interfering RNAs (siRNAs). The siRNAs are incorporated into an RNA-induced silencing complex (RISC) that cleaves the mRNA transcript of the endogenous target gene, thereby substantially reducing the number of mRNA transcripts to be translated into a polypeptide. Preferably, the double stranded RNA sequence corresponds to a target gene.

Another example of an RNA silencing method involves the introduction of nucleic acid sequences or parts thereof (in this case a stretch of substantially contiguous nucleotides derived from the gene of interest, or from any nucleic acid capable of encoding an orthologue, paralogue or homologue of the protein of interest) in a sense orientation into a plant. “Sense orientation” refers to a DNA sequence that is homologous to an mRNA transcript thereof. Introduced into a plant would therefore be at least one copy of the nucleic acid sequence. The additional nucleic acid sequence will reduce expression of the endogenous gene, giving rise to a phenomenon known as co-suppression. The reduction of gene expression will be more pronounced if several additional copies of a nucleic acid sequence are introduced into the plant, as there is a positive correlation between high transcript levels and the triggering of co-suppression.

Another example of an RNA silencing method involves the use of antisense nucleic acid sequences. An “antisense” nucleic acid sequence comprises a nucleotide sequence that is complementary to a “sense” nucleic acid sequence encoding a protein, i.e. complementary to the coding strand of a double-stranded cDNA molecule or complementary to an mRNA transcript sequence. The antisense nucleic acid sequence is preferably complementary to the endogenous gene to be silenced. The complementarity may be located in the “coding region” and/or in the “non-coding region” of a gene. The term “coding region” refers to a region of the nucleotide sequence comprising codons that are translated into amino acid residues. The term “non-coding region” refers to 5′ and 3′ sequences that flank the coding region that are transcribed but not translated into amino acids (also referred to as 5′ and 3′ untranslated regions).

Antisense nucleic acid sequences can be designed according to the rules of Watson and Crick base pairing. The antisense nucleic acid sequence may be complementary to the entire nucleic acid sequence (in this case a stretch of substantially contiguous nucleotides derived from the gene of interest, or from any nucleic acid capable of encoding an orthologue, paralogue or homologue of the protein of interest), but may also be an oligonucleotide that is antisense to only a part of the nucleic acid sequence (including the mRNA 5′ and 3′ UTR). For example, the antisense oligonucleotide sequence may be complementary to the region surrounding the translation start site of an mRNA transcript encoding a polypeptide. The length of a suitable antisense oligonucleotide sequence is known in the art and may start from about 50, 45, 40, 35, 30, 25, 20, 15 or 10 nucleotides in length or less. An antisense nucleic acid sequence according to the invention may be constructed using chemical synthesis and enzymatic ligation reactions using methods known in the art. For example, an antisense nucleic acid sequence (e.g., an antisense oligonucleotide sequence) may be chemically synthesized using naturally occurring nucleotides or variously modified nucleotides designed to increase the biological stability of the molecules or to increase the physical stability of the duplex formed between the antisense and sense nucleic acid sequences, e.g., phosphorothioate derivatives and acridine substituted nucleotides may be used. Examples of modified nucleotides that may be used to generate the antisense nucleic acid sequences are well known in the art. Known nucleotide modifications include methylation, cyclization and ‘caps’ and substitution of one or more of the naturally occurring nucleotides with an analogue such as inosine. Other modifications of nucleotides are well known in the art.

The antisense nucleic acid sequence can be produced biologically using an expression vector into which a nucleic acid sequence has been subcloned in an antisense orientation (i.e., RNA transcribed from the inserted nucleic acid will be of an antisense orientation to a target nucleic acid of interest). Preferably, production of antisense nucleic acid sequences in plants occurs by means of a stably integrated nucleic acid construct comprising a promoter, an operably linked antisense oligonucleotide, and a terminator.

The nucleic acid molecules used for silencing in the methods of the invention (whether introduced into a plant or generated in situ) hybridize with or bind to mRNA transcripts and/or genomic DNA encoding a polypeptide to thereby inhibit expression of the protein, e.g., by inhibiting transcription and/or translation. The hybridization can be by conventional nucleotide complementarity to form a stable duplex, or, for example, in the case of an antisense nucleic acid sequence which binds to DNA duplexes, through specific interactions in the major groove of the double helix. Antisense nucleic acid sequences may be introduced into a plant by transformation or direct injection at a specific tissue site. Alternatively, antisense nucleic acid sequences can be modified to target selected cells and then administered systemically. For example, for systemic administration, antisense nucleic acid sequences can be modified such that they specifically bind to receptors or antigens expressed on a selected cell surface, e.g., by linking the antisense nucleic acid sequence to peptides or antibodies which bind to cell surface receptors or antigens. The antisense nucleic acid sequences can also be delivered to cells using the vectors described herein.

According to a further aspect, the antisense nucleic acid sequence is an a-anomeric nucleic acid sequence. An a-anomeric nucleic acid sequence forms specific double-stranded hybrids with complementary RNA in which, contrary to the usual b-units, the strands run parallel to each other (Gaultier et al. (1987) Nucl Ac Res 15: 6625-6641). The antisense nucleic acid sequence may also comprise a 2′-o-methylribonucleotide (Inoue et al. (1987) Nucl Ac Res 15, 6131-6148) or a chimeric RNA-DNA analogue (Inoue et al. (1987) FEBS Lett. 215, 327-330).

The reduction or substantial elimination of endogenous gene expression may also be performed using ribozymes. Ribozymes are catalytic RNA molecules with ribonuclease activity that are capable of cleaving a single-stranded nucleic acid sequence, such as an mRNA, to which they have a complementary region. Thus, ribozymes (e.g., hammerhead ribozymes (described in Haselhoff and Gerlach (1988) Nature 334, 585-591) can be used to catalytically cleave mRNA transcripts encoding a polypeptide, thereby substantially reducing the number of mRNA transcripts to be translated into a polypeptide. A ribozyme having specificity for a nucleic acid sequence can be designed (see for example: Cech et al. U.S. Pat. No. 4,987,071; and Cech et al. U.S. Pat. No. 5,116,742). Alternatively, mRNA transcripts corresponding to a nucleic acid sequence can be used to select a catalytic RNA having a specific ribonuclease activity from a pool of RNA molecules (Bartel and Szostak (1993) Science 261, 1411-1418). The use of ribozymes for gene silencing in plants is known in the art (e.g., Atkins et al. (1994) WO 94/00012; Lenne et al. (1995) WO 95/03404; Lutziger et al. (2000) WO 00/00619; Prinsen et al. (1997) WO 97/13865 and Scott et al. (1997) WO 97/38116).

Gene silencing may also be achieved by insertion mutagenesis (for example, T-DNA insertion or transposon insertion) or by strategies as described by, among others, Angell and Baulcombe ((1999) Plant J 20(3): 357-62), (Amplicon VIGS WO 98/36083), or Baulcombe (WO 99/15682).

Gene silencing may also occur if there is a mutation on an endogenous gene and/or a mutation on an isolated gene/nucleic acid subsequently introduced into a plant. The reduction or substantial elimination may be caused by a non-functional polypeptide. For example, a polypeptide may bind to various interacting proteins; one or more mutation(s) and/or truncation(s) may therefore provide for a polypeptide that is still able to bind interacting proteins (such as receptor proteins) but that cannot exhibit its normal function (such as signalling ligand).

A further approach to gene silencing is by targeting nucleic acid sequences complementary to the regulatory region of the gene (e.g., the promoter and/or enhancers) to form triple helical structures that prevent transcription of the gene in target cells. See Helene, C., Anticancer Drug Res. 6, 569-84, 1991; Helene et al., Ann. N.Y. Acad. Sci. 660, 27-36 1992; and Maher, L. J. Bioassays 14, 807-15, 1992.

Other methods, such as the use of antibodies directed to an endogenous polypeptide for inhibiting its function in planta, or interference in the signalling pathway in which a polypeptide is involved, will be well known to the skilled man. In particular, it can be envisaged that manmade molecules may be useful for inhibiting the biological function of a target polypeptide, or for interfering with the signalling pathway in which the target polypeptide is involved.

Alternatively, a screening program may be set up to identify in a plant population natural variants of a gene, which variants encode polypeptides with reduced activity. Such natural variants may also be used for example, to perform homologous recombination.

Artificial and/or natural microRNAs (miRNAs) may be used to knock out gene expression and/or mRNA translation. Endogenous miRNAs are single stranded small RNAs of typically 19-24 nucleotides long. They function primarily to regulate gene expression and/or mRNA translation. Most plant microRNAs (miRNAs) have perfect or near-perfect complementarity with their target sequences. However, there are natural targets with up to five mismatches. They are processed from longer non-coding RNAs with characteristic fold-back structures by double-strand specific RNases of the Dicer family. Upon processing, they are incorporated in the RNA-induced silencing complex (RISC) by binding to its main component, an Argonaute protein. MiRNAs serve as the specificity components of RISC, since they base-pair to target nucleic acids, mostly mRNAs, in the cytoplasm. Subsequent regulatory events include target mRNA cleavage and destruction and/or translational inhibition. Effects of miRNA overexpression are thus often reflected in decreased mRNA levels of target genes.

Artificial microRNAs (amiRNAs), which are typically 21 nucleotides in length, can be genetically engineered specifically to negatively regulate gene expression of single or multiple genes of interest. Determinants of plant microRNA target selection are well known in the art. Empirical parameters for target recognition have been defined and can be used to aid in the design of specific amiRNAs, Schwab R, 2005. Convenient tools for design and generation of amiRNAs and their precursors are also available to the public, Schwab et al., 2006.

For optimal performance, the gene silencing techniques used for reducing expression in a plant of an endogenous gene requires the use of nucleic acid sequences from monocotyledonous plants for transformation of monocotyledonous plants, and from dicotyledonous plants for transformation of dicotyledonous plants. Preferably, a nucleic acid sequence from any given plant species is introduced into that same species. For example, a nucleic acid sequence from rice is transformed into a rice plant. However, it is not an absolute requirement that the nucleic acid sequence to be introduced originates from the same plant species as the plant in which it will be introduced. It is sufficient that there is substantial homology between the endogenous target gene and the nucleic acid to be introduced.

Described above are examples of various methods for the reduction or substantial elimination of expression in a plant of an endogenous gene. A person skilled in the art would readily be able to adapt the aforementioned methods for silencing so as to achieve reduction of expression of an endogenous gene in a whole plant or in parts thereof through the use of an appropriate promoter, for example.

Selectable Marker (Gene)/Reporter Gene

“Selectable marker”, “selectable marker gene” or “reporter gene” includes any gene that confers a phenotype on a cell in which it is expressed to facilitate the identification and/or selection of cells that are transfected or transformed with a nucleic acid construct of the invention. These marker genes enable the identification of a successful transfer of the nucleic acid molecules via a series of different principles. Suitable markers may be selected from markers that confer antibiotic or herbicide resistance, that introduce a new metabolic trait or that allow visual selection. Examples of selectable marker genes include genes conferring resistance to antibiotics (such as nptII that phosphorylates neomycin and kanamycin, or hpt, phosphorylating hygromycin, or genes conferring resistance to, for example, bleomycin, streptomycin, tetracyclin, chloramphenicol, ampicillin, gentamycin, geneticin (G418), spectinomycin or blasticidin), to herbicides (for example bar which provides resistance to Basta®; aroA or gox providing resistance against glyphosate, or the genes conferring resistance to, for example, imidazolinone, phosphinothricin or sulfonylurea), or genes that provide a metabolic trait (such as manA that allows plants to use mannose as sole carbon source or xylose isomerase for the utilisation of xylose, or antinutritive markers such as the resistance to 2-deoxyglucose). Expression of visual marker genes results in the formation of colour (for example β-glucuronidase, GUS or β-galactosidase with its coloured substrates, for example X-Gal), luminescence (such as the luciferin/luceferase system) or fluorescence (Green Fluorescent Protein, GFP, and derivatives thereof). This list represents only a small number of possible markers. The skilled worker is familiar with such markers. Different markers are preferred, depending on the organism and the selection method.

It is known that upon stable or transient integration of nucleic acids into plant cells, only a minority of the cells takes up the foreign DNA and, if desired, integrates it into its genome, depending on the expression vector used and the transfection technique used. To identify and select these integrants, a gene coding for a selectable marker (such as the ones described above) is usually introduced into the host cells together with the gene of interest. These markers can for example be used in mutants in which these genes are not functional by, for example, deletion by conventional methods. Furthermore, nucleic acid molecules encoding a selectable marker can be introduced into a host cell on the same vector that comprises the sequence encoding the polypeptides of the invention or used in the methods of the invention, or else in a separate vector. Cells which have been stably transfected with the introduced nucleic acid can be identified for example by selection (for example, cells which have integrated the selectable marker survive whereas the other cells die).

Since the marker genes, particularly genes for resistance to antibiotics and herbicides, are no longer required or are undesired in the transgenic host cell once the nucleic acids have been introduced successfully, the process according to the invention for introducing the nucleic acids advantageously employs techniques which enable the removal or excision of these marker genes. One such a method is what is known as co-transformation. The co-transformation method employs two vectors simultaneously for the transformation, one vector bearing the nucleic acid according to the invention and a second bearing the marker gene(s). A large proportion of transformants receives or, in the case of plants, comprises (up to 40% or more of the transformants), both vectors. In case of transformation with Agrobacteria, the transformants usually receive only a part of the vector, i.e. the sequence flanked by the T-DNA, which usually represents the expression cassette. The marker genes can subsequently be removed from the transformed plant by performing crosses. In another method, marker genes integrated into a transposon are used for the transformation together with desired nucleic acid (known as the Ac/Ds technology). The transformants can be crossed with a transposase source or the transformants are transformed with a nucleic acid construct conferring expression of a transposase, transiently or stable. In some cases (approx. 10%), the transposon jumps out of the genome of the host cell once transformation has taken place successfully and is lost. In a further number of cases, the transposon jumps to a different location. In these cases the marker gene must be eliminated by performing crosses. In microbiology, techniques were developed which make possible, or facilitate, the detection of such events. A further advantageous method relies on what is known as recombination systems; whose advantage is that elimination by crossing can be dispensed with. The best-known system of this type is what is known as the Cre/lox system. Cre1 is a recombinase that removes the sequences located between the loxP sequences. If the marker gene is integrated between the loxP sequences, it is removed once transformation has taken place successfully, by expression of the recombinase. Further recombination systems are the HIN/HIX, FLP/FRT and REP/STB system (Tribble et al., J. Biol. Chem., 275, 2000: 22255-22267; Velmurugan et al., J. Cell Biol., 149, 2000: 553-566). A site-specific integration into the plant genome of the nucleic acid sequences according to the invention is possible. Naturally, these methods can also be applied to microorganisms such as yeast, fungi or bacteria.

Transgenic/Transgene/Recombinant

For the purposes of the invention, “transgenic”, “transgene” or “recombinant” means with regard to, for example, a nucleic acid sequence, an expression cassette, gene construct or a vector comprising the nucleic acid sequence or an organism transformed with the nucleic acid sequences, expression cassettes or vectors according to the invention, all those constructions brought about by recombinant methods in which either

-   -   (a) the nucleic acid sequences encoding proteins useful in the         methods of the invention, or     -   (b) genetic control sequence(s) which is operably linked with         the nucleic acid sequence according to the invention, for         example a promoter, or     -   (c) a) and b)         are not located in their natural genetic environment or have         been modified by recombinant methods, it being possible for the         modification to take the form of, for example, a substitution,         addition, deletion, inversion or insertion of one or more         nucleotide residues. The natural genetic environment is         understood as meaning the natural genomic or chromosomal locus         in the original plant or the presence in a genomic library. In         the case of a genomic library, the natural genetic environment         of the nucleic acid sequence is preferably retained, at least in         part. The environment flanks the nucleic acid sequence at least         on one side and has a sequence length of at least 50 bp,         preferably at least 500 bp, especially preferably at least 1000         bp, most preferably at least 5000 bp. A naturally occurring         expression cassette—for example the naturally occurring         combination of the natural promoter of the nucleic acid         sequences with the corresponding nucleic acid sequence encoding         a polypeptide useful in the methods of the present invention, as         defined above—becomes a transgenic expression cassette when this         expression cassette is modified by non-natural, synthetic         (“artificial”) methods such as, for example, mutagenic         treatment. Suitable methods are described, for example, in U.S.         Pat. No. 5,565,350 or WO 00/15815.

A transgenic plant for the purposes of the invention is thus understood as meaning, as above, that the nucleic acids used in the method of the invention are not at their natural locus in the genome of said plant, it being possible for the nucleic acids to be expressed homologously or heterologously. However, as mentioned, transgenic also means that, while the nucleic acids according to the invention or used in the inventive method are at their natural position in the genome of a plant, the sequence has been modified with regard to the natural sequence, and/or that the regulatory sequences of the natural sequences have been modified. Transgenic is preferably understood as meaning the expression of the nucleic acids according to the invention at an unnatural locus in the genome, i.e. homologous or, preferably, heterologous expression of the nucleic acids takes place. Preferred transgenic plants are mentioned herein.

Transformation

The term “introduction” or “transformation” as referred to herein encompasses the transfer of an exogenous polynucleotide into a host cell, irrespective of the method used for transfer. Plant tissue capable of subsequent clonal propagation, whether by organogenesis or embryogenesis, may be transformed with a genetic construct of the present invention and a whole plant regenerated there from. The particular tissue chosen will vary depending on the clonal propagation systems available for, and best suited to, the particular species being transformed. Exemplary tissue targets include leaf disks, pollen, embryos, cotyledons, hypocotyls, megagametophytes, callus tissue, existing meristematic tissue (e.g., apical meristem, axillary buds, and root meristems), and induced meristem tissue (e.g., cotyledon meristem and hypocotyl meristem). The polynucleotide may be transiently or stably introduced into a host cell and may be maintained non-integrated, for example, as a plasmid. Alternatively, it may be integrated into the host genome. The resulting transformed plant cell may then be used to regenerate a transformed plant in a manner known to persons skilled in the art.

The transfer of foreign genes into the genome of a plant is called transformation. Transformation of plant species is now a fairly routine technique. Advantageously, any of several transformation methods may be used to introduce the gene of interest into a suitable ancestor cell. The methods described for the transformation and regeneration of plants from plant tissues or plant cells may be utilized for transient or for stable transformation. Transformation methods include the use of liposomes, electroporation, chemicals that increase free DNA uptake, injection of the DNA directly into the plant, particle gun bombardment, transformation using viruses or pollen and microprojection. Methods may be selected from the calcium/polyethylene glycol method for protoplasts (Krens, F. A. et al., (1982) Nature 296, 72-74; Negrutiu I et al. (1987) Plant Mol Biol 8: 363-373); electroporation of protoplasts (Shillito R. D. et al. (1985) Bio/Technol 3, 1099-1102); microinjection into plant material (Crossway A et al., (1986) Mol. Gen. Genet. 202: 179-185); DNA or RNA-coated particle bombardment (Klein T M et al., (1987) Nature 327: 70) infection with (non-integrative) viruses and the like. Transgenic plants, including transgenic crop plants, are preferably produced via Agrobacterium-mediated transformation. An advantageous transformation method is the transformation in planta. To this end, it is possible, for example, to allow the agrobacteria to act on plant seeds or to inoculate the plant meristem with agrobacteria. It has proved particularly expedient in accordance with the invention to allow a suspension of transformed agrobacteria to act on the intact plant or at least on the flower primordia. The plant is subsequently grown on until the seeds of the treated plant are obtained (Clough and Bent, Plant J. (1998) 16, 735-743). Methods for Agrobacterium-mediated transformation of rice include well known methods for rice transformation, such as those described in any of the following: European patent application EP 1198985 A1, Aldemita and Hodges (Planta 199: 612-617, 1996); Chan et al. (Plant Mol Biol 22 (3): 491-506, 1993), Hiei et al. (Plant J 6 (2): 271-282, 1994), which disclosures are incorporated by reference herein as if fully set forth. In the case of corn transformation, the preferred method is as described in either Ishida et al. (Nat. Biotechnol 14(6): 745-50, 1996) or Frame et al. (Plant Physiol 129(1): 13-22, 2002), which disclosures are incorporated by reference herein as if fully set forth. Said methods are further described by way of example in B. Jenes et al., Techniques for Gene Transfer, in: Transgenic Plants, Vol. 1, Engineering and Utilization, eds. S. D. Kung and R. Wu, Academic Press (1993) 128-143 and in Potrykus Annu. Rev. Plant Physiol. Plant Molec. Biol. 42 (1991) 205-225). The nucleic acids or the construct to be expressed is preferably cloned into a vector, which is suitable for transforming Agrobacterium tumefaciens, for example pBin19 (Bevan et al., Nucl. Acids Res. 12 (1984) 8711). Agrobacteria transformed by such a vector can then be used in known manner for the transformation of plants, such as plants used as a model, like Arabidopsis (Arabidopsis thaliana is within the scope of the present invention not considered as a crop plant), or crop plants such as, by way of example, tobacco plants, for example by immersing bruised leaves or chopped leaves in an agrobacterial solution and then culturing them in suitable media. The transformation of plants by means of Agrobacterium tumefaciens is described, for example, by Höfgen and Willmitzer in Nucl. Acid Res. (1988) 16, 9877 or is known inter alia from F. F. White, Vectors for Gene Transfer in Higher Plants; in Transgenic Plants, Vol. 1, Engineering and Utilization, eds. S. D. Kung and R. Wu, Academic Press, 1993, pp. 15-38.

In addition to the transformation of somatic cells, which then have to be regenerated into intact plants, it is also possible to transform the cells of plant meristems and in particular those cells which develop into gametes. In this case, the transformed gametes follow the natural plant development, giving rise to transgenic plants. Thus, for example, seeds of Arabidopsis are treated with agrobacteria and seeds are obtained from the developing plants of which a certain proportion is transformed and thus transgenic [Feldman, K A and Marks M D (1987). Mol Gen Genet. 208:274-289; Feldmann K (1992). In: C Koncz, N-H Chua and J Shell, eds, Methods in Arabidopsis Research. Word Scientific, Singapore, pp. 274-289]. Alternative methods are based on the repeated removal of the inflorescences and incubation of the excision site in the center of the rosette with transformed agrobacteria, whereby transformed seeds can likewise be obtained at a later point in time (Chang (1994). Plant J. 5: 551-558; Katavic (1994). Mol Gen Genet, 245: 363-370). However, an especially effective method is the vacuum infiltration method with its modifications such as the “floral dip” method. In the case of vacuum infiltration of Arabidopsis, intact plants under reduced pressure are treated with an agrobacterial suspension [Bechthold, N (1993). C R Acad Sci Paris Life Sci, 316: 1194-1199], while in the case of the “floral dip” method the developing floral tissue is incubated briefly with a surfactant-treated agrobacterial suspension [Clough, S J and Bent, A F (1998). The Plant J. 16, 735-743]. A certain proportion of transgenic seeds are harvested in both cases, and these seeds can be distinguished from non-transgenic seeds by growing under the above-described selective conditions. In addition the stable transformation of plastids is of advantages because plastids are inherited maternally is most crops reducing or eliminating the risk of transgene flow through pollen. The transformation of the chloroplast genome is generally achieved by a process which has been schematically displayed in Klaus et al., 2004 [Nature Biotechnology 22 (2), 225-229]. Briefly the sequences to be transformed are cloned together with a selectable marker gene between flanking sequences homologous to the chloroplast genome. These homologous flanking sequences direct site specific integration into the plastome. Plastidal transformation has been described for many different plant species and an overview is given in Bock (2001) Transgenic plastids in basic research and plant biotechnology. J Mol. Biol. 2001 Sep. 21; 312 (3):425-38 or Maliga, P (2003) Progress towards commercialization of plastid transformation technology. Trends Biotechnol. 21, 20-28. Further biotechnological progress has recently been reported in form of marker free plastid transformants, which can be produced by a transient co-integrated maker gene (Klaus et al., 2004, Nature Biotechnology 22(2), 225-229).

T-DNA Activation Taming

T-DNA activation tagging (Hayashi et al. Science (1992) 1350-1353), involves insertion of T-DNA, usually containing a promoter (may also be a translation enhancer or an intron), in the genomic region of the gene of interest or 10 kb up- or downstream of the coding region of a gene in a configuration such that the promoter directs expression of the targeted gene.

Typically, regulation of expression of the targeted gene by its natural promoter is disrupted and the gene falls under the control of the newly introduced promoter. The promoter is typically embedded in a T-DNA. This T-DNA is randomly inserted into the plant genome, for example, through Agrobacterium infection and leads to modified expression of genes near the inserted T-DNA. The resulting transgenic plants show dominant phenotypes due to modified expression of genes close to the introduced promoter.

TILLING

TILLING (Targeted Induced Local Lesions In Genomes) is a mutagenesis technology useful to generate and/or identify nucleic acids encoding proteins with modified expression and/or activity. TILLING also allows selection of plants carrying such mutant variants. These mutant variants may exhibit modified expression, either in strength or in location or in timing (if the mutations affect the promoter for example). These mutant variants may exhibit higher activity than that exhibited by the gene in its natural form. TILLING combines high-density mutagenesis with high-throughput screening methods. The steps typically followed in TILLING are: (a) EMS mutagenesis (Redei G P and Koncz C (1992) In Methods in Arabidopsis Research, Koncz C, Chua N H, Schell J, eds. Singapore, World Scientific Publishing Co, pp. 16-82; Feldmann et al., (1994) In Meyerowitz E M, Somerville C R, eds, Arabidopsis. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., pp 137-172; Lightner J and Caspar T (1998) In J Martinez-Zapater, J Salinas, eds, Methods on Molecular Biology, Vol. 82. Humana Press, Totowa, N.J., pp 91-104); (b) DNA preparation and pooling of individuals; (c) PCR amplification of a region of interest; (d) denaturation and annealing to allow formation of heteroduplexes; (e) DHPLC, where the presence of a heteroduplex in a pool is detected as an extra peak in the chromatogram; (f) identification of the mutant individual; and (g) sequencing of the mutant PCR product. Methods for TILLING are well known in the art (McCallum et al., (2000) Nat Biotechnol 18: 455-457; reviewed by Stemple (2004) Nat Rev Genet. 5(2): 145-50).

Homologous Recombination

Homologous recombination allows introduction in a genome of a selected nucleic acid at a defined selected position. Homologous recombination is a standard technology used routinely in biological sciences for lower organisms such as yeast or the moss Physcomitrella. Methods for performing homologous recombination in plants have been described not only for model plants (Offring a et al. (1990) EMBO J. 9(10): 3077-84) but also for crop plants, for example rice (Terada et al. (2002) Nat Biotech 20(10): 1030-4; lida and Terada (2004) Curr Opin Biotech 15(2): 132-8).

Yield

The term “yield” in general means a measurable produce of economic value, typically related to a specified crop, to an area, and to a period of time. Individual plant parts directly contribute to yield based on their number, size and/or weight, or the actual yield is the yield per acre for a crop and year, which is determined by dividing total production (includes both harvested and appraised production) by planted acres.

Early Vigour

Early vigour (active healthy well-balanced growth especially during early stages of plant growth) may result from increased plant fitness due to, for example, the plants being better adapted to their environment (i.e. optimizing the use of energy resources and partitioning between shoot and root). Plants having early vigour also show increased seedling survival and a better establishment of the crop, which often results in highly uniform fields (with the crop growing in uniform manner, i.e. with the majority of plants reaching the various stages of development at substantially the same time), and often better and higher yield. Therefore, early vigour may be determined by measuring various factors, such as thousand kernel weight, percentage germination, percentage emergence, seedling growth, seedling height, root length, root and shoot biomass and many more.

Increase/Improve/Enhance

The terms “increase”, “improve” or “enhance” are interchangeable and shall mean in the sense of the application at least a 5%, 6%, 7%, 8%, 9% or 10%, preferably at least 15% or 20%, more preferably 25%, 30%, 35% or 40% more yield and/or growth in comparison to control plants as defined herein.

Seed Yield

Increased seed yield may manifest itself as one or more of the following: a) an increase in seed biomass (total seed weight) which may be on an individual seed basis and/or per plant and/or per hectare or acre; b) increased number of flowers per plant; c) increased number of (filled) seeds; d) increased seed filling rate (which is expressed as the ratio between the number of filled seeds divided by the total number of seeds); e) increased harvest index, which is expressed as a ratio of the yield of harvestable parts, such as seeds, divided by the total biomass; and f) increased thousand kernel weight (TKW), which is extrapolated from the number of filled seeds counted and their total weight. An increased TKW may result from an increased seed size and/or seed weight, and may also result from an increase in embryo and/or endosperm size.

An increase in seed yield may also be manifested as an increase in seed size and/or seed volume. Furthermore, an increase in seed yield may also manifest itself as an increase in seed area and/or seed length and/or seed width and/or seed perimeter. Increased yield may also result in modified architecture, or may occur because of modified architecture.

Plant

The term “plant” as used herein encompasses whole plants, ancestors and progeny of the plants and plant parts, including seeds, shoots, stems, leaves, roots (including tubers), flowers, and tissues and organs, wherein each of the aforementioned comprise the gene/nucleic acid of interest. The term “plant” also encompasses plant cells, suspension cultures, callus tissue, embryos, meristematic regions, gametophytes, sporophytes, pollen and microspores, again wherein each of the aforementioned comprises the gene/nucleic acid of interest.

Plants that are particularly useful in the methods of the invention include all plants which belong to the superfamily Viridiplantae, in particular monocotyledonous and dicotyledonous plants including fodder or forage legumes, ornamental plants, food crops, trees or shrubs selected from the list comprising Acer spp., Actinidia spp., Abelmoschus spp., Agave sisalana, Agropyron spp., Agrostis stolonifera, Allium spp., Amaranthus spp., Ammophila arenaria, Ananas comosus, Annona spp., Apium graveolens, Arachis spp, Artocarpus spp., Asparagus officinalis, Avena spp. (e.g. Avena sativa, Avena fatua, Avena byzantina, Avena fatua var. sativa, Avena hybrida), Averrhoa carambola, Bambusa sp., Benincasa hispida, Bertholletia excelsea, Beta vulgaris, Brassica spp. (e.g. Brassica napus, Brassica rapa ssp. [canola, oilseed rape, turnip rape]), Cadaba farinosa, Camellia sinensis, Canna indica, Cannabis sativa, Capsicum spp., Carex elata, Carica papaya, Carissa macrocarpa, Carya spp., Carthamus tinctorius, Castanea spp., Ceiba pentandra, Cichorium endivia, Cinnamomum spp., Citrullus lanatus, Citrus spp., Cocos spp., Coffea spp., Colocasia esculenta, Cola spp., Corchorus sp., Coriandrum sativum, Corylus spp., Crataegus spp., Crocus sativus, Cucurbita spp., Cucumis spp., Cynara spp., Daucus carota, Desmodium spp., Dimocarpus longan, Dioscorea spp., Diospyros spp., Echinochloa spp., Elaeis (e.g. Elaeis guineensis, Elaeis oleifera), Eleusine coracana, Erianthus sp., Eriobotrya japonica, Eucalyptus sp., Eugenia uniflora, Fagopyrum spp., Fagus spp., Festuca arundinacea, Ficus carica, Fortunella spp., Fragaria spp., Ginkgo biloba, Glycine spp. (e.g. Glycine max, Soja hispida or Soja max), Gossypium hirsutum, Helianthus spp. (e.g. Helianthus annuus), Hemerocallis fulva, Hibiscus spp., Hordeum spp. (e.g. Hordeum vulgare), Ipomoea batatas, Juglans spp., Lactuca sativa, Lathyrus spp., Lens culinaris, Linum usitatissimum, Litchi chinensis, Lotus spp., Luffa acutangula, Lupinus spp., Luzula sylvatica, Lycopersicon spp. (e.g. Lycopersicon esculentum, Lycopersicon lycopersicum, Lycopersicon pyriforme), Macrotyloma spp., Malus spp., Malpighia emarginata, Mammea americana, Mangifera indica, Manihot spp., Manilkara zapota, Medicago sativa, Melilotus spp., Mentha spp., Miscanthus sinensis, Momordica spp., Morus nigra, Musa spp., Nicotiana spp., Olea spp., Opuntia spp., Ornithopus spp., Oryza spp. (e.g. Oryza sativa, Oryza latifolia), Panicum miliaceum, Panicum virgatum, Passiflora edulis, Pastinaca sativa, Pennisetum sp., Persea spp., Petroselinum crispum, Phalaris arundinacea, Phaseolus spp., Phleum pratense, Phoenix spp., Phragmites australis, Physalis spp., Pinus spp., Pistacia vera, Pisum spp., Poa spp., Populus spp., Prosopis spp., Prunus spp., Psidium spp., Punica granatum, Pyrus communis, Quercus spp., Raphanus sativus, Rheum rhabarbarum, Ribes spp., Ricinus communis, Rubus spp., Saccharum spp., Salix sp., Sambucus spp., Secale cereale, Sesamum spp., Sinapis sp., Solanum spp. (e.g. Solanum tuberosum, Solanum integrifolium or Solanum lycopersicum), Sorghum bicolor, Spinacia spp., Syzygium spp., Tagetes spp., Tamarindus indica, Theobroma cacao, Trifolium spp., Triticosecale rimpaui, Triticum spp. (e.g. Triticum aestivum, Triticum durum, Triticum turgidum, Triticum hybernum, Triticum macha, Triticum sativum or Triticum vulgare), Tropaeolum minus, Tropaeolum majus, Vaccinium spp., Vicia spp., Vigna spp., Viola odorata, Vitis spp., Zea mays, Zizania palustris, Ziziphus spp., amongst others.

DETAILED DESCRIPTION OF THE INVENTION Detailed Description for HAL3

According to a first embodiment of the present invention, there is provided a method for increasing plant yield relative to control plants, comprising preferentially increasing expression of a nucleic acid encoding a HAL3 polypeptide in expanding tissues of a plant.

Any reference hereinafter to a “protein useful in the methods of the invention” is taken to mean a HAL3 polypeptide as defined herein. Any reference hereinafter to a “nucleic acid useful in the methods of the invention” is taken to mean a nucleic acid capable of encoding such an HAL3 polypeptide. The nucleic acid to be introduced into a plant (and therefore useful in performing the methods of the invention) is any nucleic acid encoding the type of protein which will now be described, hereafter also named “HAL3 nucleic acid” or “HAL3 gene”.

A “reference”, “reference plant”, “control”, “control plant”, “wild type” or “wild type plant” is in particular a cell, a tissue, an organ, a plant, or a part thereof, which was not produced according to the method of the invention. Accordingly, the terms “wild type”, “control” or “reference” are exchangeable and can be a cell or a part of the plant such as an organelle or tissue, or a plant, which was not modified or treated according to the herein described method according to the invention. Accordingly, the cell or a part of the plant such as an organelle or a plant used as wild type, control or reference corresponds to the cell, plant or part thereof as much as possible and is in any other property but in the result of the process of the invention as identical to the subject matter of the invention as possible. Thus, the wild type, control or reference is treated identically or as identical as possible, saying that only conditions or properties might be different which do not influence the quality of the tested property. That means in other words that the wild type denotes (1) a plant, which carries the unaltered or not modulated form of a gene or allele or (2) the starting material/plant from which the plants produced by the process or method of the invention are derived.

Preferably, any comparison between the wild type plants and the plants produced by the method of the invention is carried out under analogous conditions. The term “analogous conditions” means that all conditions such as, for example, culture or growing conditions, assay conditions (such as buffer composition, temperature, substrates, pathogen strain, concentrations and the like) are kept identical between the experiments to be compared.

The “reference”, “control”, or “wild type” is preferably a subject, e.g. an organelle, a cell, a tissue, a plant, which was not modulated, modified or treated according to the herein described process of the invention and is in any other property as similar to the subject matter of the invention as possible. The reference, control or wild type is in its genome, transcriptome, proteome or metabolome as similar as possible to the subject of the present invention. Preferably, the term “reference-” “control-” or “wild type-”-organelle, -cell, -tissue or plant, relates to an organelle, cell, tissue or plant, which is nearly genetically identical to the organelle, cell, tissue or plant, of the present invention or a part thereof preferably 95%, more preferred are 98%, even more preferred are 99,00%, in particular 99,10%, 99,30%, 99,50%, 99,70%, 99,90%, 99,99%, 99, 999% or more. Most preferable the “reference”, “control”, or “wild type” is preferably a subject, e.g. an organelle, a cell, a tissue, a plant, which is genetically identical to the plant, cell organelle used according to the method of the invention except that nucleic acid molecules or the gene product encoded by them are changed, modulated or modified according to the inventive method.

In case, a control, reference or wild type differing from the subject of the present invention only by not being subject of the method of the invention can not be provided, a control, reference or wild type can be a plant in which the cause for the modulation of the activity conferring the increase of the metabolites as described under examples.

The increase referred to the activity of the polypeptide amounts in a cell, a tissue, a organelle, an organ or an organism or a part thereof preferably to at least 5%, preferably to at least 10% or at to least 15%, especially preferably to at least 20%, 25%, 30% or more, very especially preferably are to at least 40%, 50% or 60%, most preferably are to at least 70% or more in comparison to the control, reference or wild type.

The term “increased yield” is taken to mean an increase in biomass (weight) of one or more parts of a plant, which may include aboveground (harvestable) parts and/or (harvestable) parts below ground. Preferably, the increase in yield is at least 10% over the yield of corresponding wild type plants.

In particular, such harvestable parts are seeds, and performance of the methods of the invention results in plants having increased seed yield relative to the seed yield of control plants.

The term “expression” or “gene expression” means the appearance of a phenotypic trait as a consequence of the transcription of a specific gene or specific genes. The term “expression” or “gene expression” in particular means the transcription of a gene or genes into structural RNA (rRNA, tRNA) or mRNA with subsequent translation of the latter into a protein. The process includes transcription of DNA, processing of the resulting mRNA product and its translation into an active protein.

Performance of the methods of the invention gives plants having enhanced yield-related traits. In particular performance of the methods of the invention gives plants having increased yield, especially increased seed yield relative to control plants. The terms “yield” and “seed yield” are described in more detail in the “definitions” section herein.

Reference herein to enhanced yield-related traits is taken to mean an increase in biomass (weight) of one or more parts of a plant, which may include aboveground (harvestable) parts and/or (harvestable) parts below ground. In particular, such harvestable parts are seeds, and performance of the methods of the invention results in plants having increased seed yield relative to the seed yield of suitable control plants.

Taking corn as an example, a yield increase may be manifested as one or more of the following: increase in the number of plants per hectare or acre, an increase in the number of ears per plant, an increase in the number of rows, number of kernels per row, kernel weight, thousand kernel weight, ear length/diameter, increase in the seed filling rate (which is the number of filled seeds divided by the total number of seeds and multiplied by 100), among others. Taking rice as an example, a yield increase may manifest itself as an increase in one or more of the following: number of plants per hectare or acre, number of panicles per plant, number of spikelets per panicle, number of flowers (florets) per panicle (which is expressed as a ratio of the number of filled seeds over the number of primary panicles), increase in the seed filling rate (which is the number of filled seeds divided by the total number of seeds and multiplied by 100), increase in thousand kernel weight, among others.

According to a preferred feature of the present invention, performance of the methods of the invention gives plants having increased seed yield relative to control plants. Therefore according to the present invention, there is provided a method for increasing seed yield in plants relative to the seed yield of control plants, the method comprising preferentially increasing expression of a nucleic acid encoding a HAL3 polypeptide in shoot tissues, preferably in expanding tissues of a plant shoot.

Since the transgenic plants according to the present invention have increased yield, it is likely that these plants exhibit an increased growth rate (during at least part of their life cycle), relative to the growth rate of control plants at a corresponding stage in their life cycle.

The increased growth rate may be specific to one or more parts of a plant (including seeds), or may be throughout substantially the whole plant. Plants having an increased growth rate may have a shorter life cycle. The life cycle of a plant may be taken to mean the time needed to grow from a dry mature seed up to the stage where the plant has produced dry mature seeds, similar to the starting material. This life cycle may be influenced by factors such as early vigour, growth rate, greenness index, flowering time and speed of seed maturation. The increase in growth rate may take place at one or more stages in the life cycle of a plant or during substantially the whole plant life cycle. Increased growth rate during the early stages in the life cycle of a plant may reflect enhanced vigour. The increase in growth rate may alter the harvest cycle of a plant allowing plants to be sown later and/or harvested sooner than would otherwise be possible (a similar effect may be obtained with earlier flowering time). If the growth rate is sufficiently increased, it may allow for the further sowing of seeds of the same plant species (for example sowing and harvesting of rice plants followed by sowing and harvesting of further rice plants all within one conventional growing period). Similarly, if the growth rate is sufficiently increased, it may allow for the further sowing of seeds of different plants species (for example the sowing and harvesting of corn plants followed by, for example, the sowing and optional harvesting of soybean, potato or any other suitable plant). Harvesting additional times from the same rootstock in the case of some crop plants may also be possible. Altering the harvest cycle of a plant may lead to an increase in annual biomass production per acre (due to an increase in the number of times (say in a year) that any particular plant may be grown and harvested). An increase in growth rate may also allow for the cultivation of transgenic plants in a wider geographical area than their wild-type counterparts, since the territorial limitations for growing a crop are often determined by adverse environmental conditions either at the time of planting (early season) or at the time of harvesting (late season). Such adverse conditions may be avoided if the harvest cycle is shortened. The growth rate may be determined by deriving various parameters from growth curves, such parameters may be: T-Mid (the time taken for plants to reach 50% of their maximal size) and T-90 (time taken for plants to reach 90% of their maximal size), amongst others.

According to a preferred feature of the present invention, performance of the methods of the invention gives plants having an increased growth rate relative to control plants. Therefore, according to the present invention, there is provided a method for increasing the growth rate of plants, which method comprises modulating expression, preferably increasing expression, in a plant of a nucleic acid encoding a HAL3 polypeptide as defined herein.

An increase in yield and/or growth rate occurs whether the plant is under non-stress conditions or whether the plant is exposed to various stresses compared to control plants. Plants typically respond to exposure to stress by growing more slowly. In conditions of severe stress, the plant may even stop growing altogether. Mild stress on the other hand is defined herein as being any stress to which a plant is exposed which does not result in the plant ceasing to grow altogether without the capacity to resume growth. Mild stress in the sense of the invention leads to a reduction in the growth of the stressed plants of less than 40%, 35% or 30%, preferably less than 25%, 20% or 15%, more preferably less than 14%, 13%, 12%, 11% or 10% or less in comparison to the control plant under non-stress conditions. Due to advances in agricultural practices (irrigation, fertilization, pesticide treatments) severe stresses are not often encountered in cultivated crop plants. As a consequence, the compromised growth induced by mild stress is often an undesirable feature for agriculture. Mild stresses are the everyday biotic and/or abiotic (environmental) stresses to which a plant is exposed. Abiotic stresses may be due to drought or excess water, anaerobic stress, salt stress, chemical toxicity, oxidative stress and hot, cold or freezing temperatures. The abiotic stress may be an osmotic stress caused by a water stress (particularly due to drought), salt stress, oxidative stress or an ionic stress. Biotic stresses are typically those stresses caused by pathogens, such as bacteria, viruses, fungi and insects.

In particular, the methods of the present invention may be performed under non-stress conditions or under conditions of mild drought to give plants having increased yield relative to control plants. As reported in Wang et al. (Planta (2003) 218: 1-14), abiotic stress leads to a series of morphological, physiological, biochemical and molecular changes that adversely affect plant growth and productivity. Drought, salinity, extreme temperatures and oxidative stress are known to be interconnected and may induce growth and cellular damage through similar mechanisms. Rabbani et al. (Plant Physiol (2003) 133: 1755-1767) describes a particularly high degree of “cross talk” between drought stress and high-salinity stress. For example, drought and/or salinisation are manifested primarily as osmotic stress, resulting in the disruption of homeostasis and ion distribution in the cell. Oxidative stress, which frequently accompanies high or low temperature, salinity or drought stress, may cause denaturing of functional and structural proteins. As a consequence, these diverse environmental stresses often activate similar cell signaling pathways and cellular responses, such as the production of stress proteins, up-regulation of anti-oxidants, accumulation of compatible solutes and growth arrest. The term “non-stress” conditions as used herein are those environmental conditions that allow optimal growth of plants. Persons skilled in the art are aware of normal soil conditions and climatic conditions for a given location.

Performance of the methods of the invention gives plants grown under non-stress conditions or under mild drought conditions increased yield relative to suitable control plants grown under comparable conditions. Therefore, according to the present invention, there is provided a method for increasing yield in plants grown under non-stress conditions or under mild drought conditions, which method comprises increasing expression in a plant of a nucleic acid encoding a HAL3 polypeptide.

Performance of the methods of the invention gives plants grown under conditions of nutrient deficiency, particularly under conditions of nitrogen deficiency, increased yield relative to control plants grown under comparable conditions. Therefore, according to the present invention, there is provided a method for increasing yield in plants grown under conditions of nutrient deficiency, which method comprises increasing expression in a plant of a nucleic acid encoding a HAL3 polypeptide. Nutrient deficiency may result from a lack or excess of nutrients such as nitrogen, phosphates and other phosphorous-containing compounds, potassium, calcium, cadmium, magnesium, manganese, iron and boron, amongst others.

According to a second preferred feature of the invention, performance of the methods of the invention gives plants having increased plant vigour relative to control plants, particularly during the early stages of plant development (typically three, four weeks post germination in the case of rice and maize, but this will vary from species to species) leading to early vigour. Therefore, according to the present invention, there is provided a method for increasing the plant early vigour, which method comprises modulating, preferably increasing expression in a plant of a nucleic acid encoding a HAL3 polypeptide. Preferably the increase in seedling vigour is achieved by expressing the nucleic acid encoding the HAL3 polypeptide under the control of a shoot specific promoter. There is also provided a method for producing plants having early vigour relative to control plants, which method comprises modulating, preferably increasing, expression in a plant of a nucleic acid encoding a HAL3 polypeptide.

Early vigour may also result from increased plant fitness due to, for example, the plants being better adapted to their environment (i.e. optimizing the use of energy resources and partitioning between shoot and root). Plants having early vigour also show increased seedling survival and a better establishment of the crop, which often results in highly uniform fields (with the crop growing in uniform manner, i.e. with the majority of plants reaching the various stages of development at substantially the same time), and often better and higher yield. Therefore, early vigour may be determined by measuring various factors, such as thousand kernel weight, percentage germination, percentage emergence, seedling growth, seedling height, root length, root and shoot biomass and many more.

The methods of the invention are advantageously applicable to any plant.

Plants that are particularly useful in the methods of the invention include all plants which belong to the superfamily Viridiplantae, in particular monocotyledonous and dicotyledonous plants including fodder or forage legumes, ornamental plants, food crops, trees or shrubs. According to a preferred embodiment of the present invention, the plant is a crop plant. Examples of crop plants include soybean, sunflower, canola, alfalfa, rapeseed, cotton, tomato, potato and tobacco. Further preferably, the plant is a monocotyledonous plant. Examples of monocotyledonous plants include sugarcane. More preferably the plant is a cereal. Examples of cereals include rice, maize, wheat, barley, millet, rye, triticale, sorghum and oats.

Other advantageous plants are selected from the group consisting of Asteraceae such as the genera Helianthus, Tagetes e.g. the species Helianthus annus [sunflower], Tagetes lucida, Tagetes erecta or Tagetes tenuifolia [Marigold], Brassicaceae such as the genera Brassica, Arabadopsis e.g. the species Brassica napus, Brassica rapa ssp. [canola, oilseed rape, turnip rape] or Arabidopsis thaliana. Fabaceae such as the genera Glycine e.g. the species Glycine max, Soja hispida or Soja max [soybean]. Linaceae such as the genera Linum e.g. the species Linum usitatissimum, [flax, linseed]; Poaceae such as the genera Hordeum, Secale, Avena, Sorghum, Oryza, Zea, Triticum e.g. the species Hordeum vulgare [barley]; Secale cereale [rye], Avena sativa, Avena fatua, Avena byzantina, Avena fatua var. sativa, Avena hybrida [oat], Sorghum bicolor [Sorghum, millet], Oryza sativa, Oryza latifolia [rice], Zea mays [corn, maize] Triticum aestivum, Triticum durum, Triticum turgidum, Triticum hybernum, Triticum macha, Triticum sativum or Triticum vulgare [wheat, bread wheat, common wheat]; Solanaceae such as the genera Solanum, Lycopersicon e.g. the species Solanum tuberosum [potato], Lycopersicon esculentum, Lycopersicon lycopersicum, Lycopersicon pyriforme, Solanum integrifolium or Solanum lycopersicum [tomato].

The term “HAL3 polypeptide” as defined herein refers to a flavoprotein belonging to the superfamily HFCD (Homo-oligomeric Flavin containing Cys Decarboxylases; Kupke J. Biol. Chem. 276, 27597-27604, 2001). These proteins share a flavin-binding motif, conserved active-site residues and are trimeric or dodecameric enzymes. HAL3 proteins preferably comprise from N-terminus to C-terminus (i) a substrate binding helix, (ii) an insertion His motif, (iii) a PXMNXXMW motif and (iv) a substrate recognition clamp (FIG. 1). These four domains are predicted to be involved in substrate binding, the insertion His motif comprises a conserved His residue that is involved in the active site whereas the sequence in the substrate recognition clamp may be somewhat variable in sequence and length (Blaesse et al., EMBO J. 19, 6299-6310, 2000). The structural features (i) to (iv) are also described in Kupke et al. (2001), which disclosure is incorporated herein by reference. Typically, HAL3 polypeptides are capable of binding of FMN cofactors.

Typically the substrate binding helix is comprised in sequence motif 1 with the following consensus sequence (SEQ ID NO: 6):

(K/R)PR(V/I) (I/L)LAA(S/T)GSVA(A/S) (I/M/V)KF (G/E/A/S) (N/S/I)L(C/V/A) (H/R/G) (C/S/I) (F/L) (T/S/C) (E/D/Q)WA(E/D)V(R/K)AV(V/A/S).

The insertion His motif, the PXMNXXMW motif and the substrate recognition clamp are part of sequence motif 2 with the following consensus sequence (SEQ ID NO: 7):

VLHIELR(R/K/Q)WAD(V/I/A) (L/M) (V/I)IAPLSANTL(G/A) KIAGG(L/M)CDNLLTC(I/V)(I/V)RAWD(Y/F) (T/S/N/D/K)KP (L/F/M/I)F(V/A)APAMNT(L/F)MW(N/S/T)NPFT(E/S/Q/A) (R/K)H(L/F/I) (X₁) (X₂) (L/I/M) (D/N/S) (E/L/Q) (L/M)G(I/V/L) (T/S/A/I)L(I/V)PP(I/V/T) (K/T/S)K (R/T/K)LACGD(Y/H)G(N/T)GAM(A/S)E wherein X₁ may be any amino acid, preferably X₁ is one of L, V, E, H, D, M, I or Q and wherein X₂ may be any amino acid, preferably X₂ is one of s, L, T, A, or V.

These motifs form part of a larger conserved region in the protein, as an example, the conserved region of Arabidopsis HAL3a is given as SEQ ID NO: 8. HAL3 polypeptides useful in the methods of the present invention have in increasing order of preference at least 65%, 70%, 75%, 80%, 85%, 90% or 95% sequence identity to the conserved region represented by SEQ ID NO: 8.

The conserved region in HAL3 proteins, as exemplified in SEQ ID NO: 8 and comprising the above described features (i) to (iv), encompasses a Flavoprotein domain which may be identified using specialised databases e.g. SMART (Schultz et al. (1998) Proc. Natl. Acad. Sci. USA 95, 5857-5864; Letunic et al. (2002) Nucleic Acids Res 30, 242-244), InterPro (Mulder et al., (2003) Nucl. Acids. Res. 31, 315-318), Prosite (Bucher and Bairoch (1994), A generalized profile syntax for biomolecular sequences motifs and its function in automatic sequence interpretation. (In) ISMB-94; Proceedings 2nd International Conference on Intelligent Systems for Molecular Biology. Altman R., Brutlag D., Karp P., Lathrop R., Searls D., Eds., pp 53-61, AAAIPress, Menlo Park; Hulo et al., Nucl. Acids. Res. 32:D134-D137, (2004)) or Pfam (Bateman et al., Nucleic Acids Research 30(1): 276-280 (2002)). This FMN-binding domain (Pfam entry PF02441, InterPro entry IPRO03382) is typically found in flavoprotein enzymes. The terms “domain” and “motif” are defined in the definitions section above.

The conserved region in SEQ ID NO: 2, as represented by SEQ ID NO: 8, may also in other HAL3 proteins be identified, using methods for the alignment of sequences for comparison as described hereinabove. In some instances, the default parameters may be adjusted to modify the stringency of the search. For example using BLAST, the statistical significance threshold (called “expect” value) for reporting matches against database sequences may be increased to show less stringent matches. This way, short nearly exact matches may be identified, including the conserved motifs 1 and 2 (SEQ ID NO: 6 and 7), or matches with one or more conservative change at any position.

HAL3 polypeptides (at least in their native form) and their homologues typically catalyse the decarboxylation of 4′-phosphopantothenoylcysteine to 4′-phosphopantetheine, a step in coenzyme A biosynthesis, which reaction may be tested in a biochemical assay; alternatively, HAL3 activity may be assayed by a complementation test with a dfp mutant E. coli strain (Kupke et al 2001; Yonamine et al 2004). The enzyme is also able to decarboxylate pantothenoylcysteine to pantothenoylcysteamine. Furthermore, the protein is involved in conferring salt and osmotic stress tolerance to plants, which feature may be useful in a bioassay for HAL3.

SEQ ID NO: 2 (encoded by SEQ ID NO: 1) is an example of a HAL3 polypeptide comprising from N-terminus to C-terminus features (i) a substrate binding helix, (ii) an insertion His motif, (iii) a PXMNXXMW motif and (iv) a substrate recognition clamp; and having in increasing order of preference at least 65%, 70%, 75%, 80%, 85%, 90% or 95% sequence identity to the conserved region represented by SEQ ID NO: 8. Further examples of HAL3 polypeptides comprising features (i) to (iv) are given in Table A in the examples section below:

Homologues of a HAL3 polypeptide may also be used to perform the methods of invention. Homologues (or homologous proteins) may readily be identified using routine techniques well known in the art, such as by sequence alignment. Methods for the alignment of sequences for comparison are well known in the art, such methods include GAP, BESTFIT, BLAST, FASTA and TFASTA. GAP uses the algorithm of Needleman and Wunsch ((1970) J Mol Biol 48: 443-453) to find the alignment of two complete sequences that maximizes the number of matches and minimizes the number of gaps. The BLAST algorithm (Altschul et al. (1990) J Mol Biol 215: 403-10) calculates percent sequence identity and performs a statistical analysis of the similarity between the two sequences. The software for performing BLAST analysis is publicly available through the National Centre for Biotechnology Information. Homologues may readily be identified using, for example, the ClustalW multiple sequence alignment algorithm (version 1.83), with the default pairwise alignment parameters, and a scoring method in percentage. Global percentages of similarity and identity may also be determined using one of the methods available in the MatGAT software package (Campanella et al., BMC Bioinformatics. 2003 Jul. 10; 4:29. MatGAT: an application that generates similarity/identity matrices using protein or DNA sequences.). Minor manual editing may be performed to optimise alignment between conserved motifs, as would be apparent to a person skilled in the art.

The sequence identity values may be determined over the entire conserved domain (as indicated above) or over the full length nucleic acid or amino acid sequence using the programs mentioned above using the default parameters.

Homologues also include orthologues and paralogues. Orthologues and paralogues may easily be found by performing a so-called reciprocal blast search. This may be done by a first BLAST involving submitting a query sequence (for example, SEQ ID NO: 1 or SEQ ID NO: 2) for a BLAST search against any sequence database, such as the publicly available NCBI database. BLASTN or TBLASTX (using standard default values) may be used when starting from a nucleotide sequence and BLASTP or TBLASTN (using standard default values) may be used when starting from a protein sequence. The BLAST results may optionally be filtered. The full-length sequences of either the filtered results or non-filtered results are then submitted to a second BLAST search (BLAST back) against sequences from the organism from which the query sequence is derived (where the query sequence is SEQ ID NO: 1 or SEQ ID NO: 2 the second BLAST would therefore be against Arabidopsis sequences). The results of the first and second BLAST searches are then compared. A paralogue is identified if a high-ranking hit from the first BLAST is from the same species as from which the query sequence is derived; an orthologue is identified if a high-ranking hit is not from the same species as from which the query sequence is derived. Preferred orthologues are orthologues of AtHAL3a (SEQ ID NO: 2), AtHAL3b (SEQ ID NO: 10) or of the long form of AtHAL3b (SEQ ID NO: 40). High-ranking hits are those having a low E-value. The lower the E-value, the more significant the score (or in other words the lower the chance that the hit was found by chance). Computation of the E-value is well known in the art. In the case of large families, ClustalW may be used, followed by a neighbour joining tree, to help visualize clustering of related genes and to identify orthologues and paralogues. In addition to E-values, comparisons are also scored by percentage identity. Percentage identity refers to the number of identical nucleotides (or amino acids) between the two compared nucleic acid (or polypeptide) sequences over a particular length. Preferably, HAL3 polypeptide homologues have in increasing order of preference at least 60%, 70%, 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% or more sequence identity or similarity (functional identity) to an unmodified HAL3 polypeptide as represented by SEQ ID NO: 2. Preferably, HAL3 polypeptide homologues are as represented by the sequences referred to in Table A.

The HAL3 polypeptide useful in the methods of the present invention may be a derivative of SEQ ID NO: 2. “Derivatives” include peptides, oligopeptides, polypeptides which may, compared to the amino acid sequence of the naturally-occurring form of the protein, such as the one presented in SEQ ID NO: 2, comprise substitutions of amino acids with non-naturally occurring amino acid residues, or additions of non-naturally occurring amino acid residues. Derivatives of the proteins as represented by the sequences listed in Table A are further examples which may be suitable for use in the methods of the invention

Examples of nucleic acids encoding HAL3 polypeptides include but are not limited to those represented by the sequences listed in Table A. Variants of nucleic acids encoding HAL3 polypeptides may be suitable for use in the methods of the invention. Suitable variants include portions of nucleic acids encoding HAL3 polypeptides and/or nucleic acids capable of hybridising with nucleic acids/genes encoding HAL3 polypeptides. Further variants include splice variants and allelic variants of nucleic acids encoding HAL3 polypeptides.

The term “portion” as defined herein refers to a piece of DNA encoding a polypeptide comprising from N-terminus to C-terminus features (i) a substrate binding helix, (ii) an insertion His motif, (iii) a PXMNXXMW motif and (iv) a substrate recognition clamp; and having in increasing order of preference at least 65%, 70%, 75%, 80%, 85%, 90% or 95% sequence identity to the conserved region represented by SEQ ID NO: 8.

A portion may be prepared, for example, by making one or more deletions to a nucleic acid encoding a HAL3 polypeptide. The portions may be used in isolated form or they may be fused to other coding (or non coding) sequences in order to, for example, produce a protein that combines several activities. When fused to other coding sequences, the resulting polypeptide produced upon translation may be bigger than that predicted for the HAL3 portion. Preferably, the portion codes for a polypeptide with substantially the same biological activity as the HAL3 polypeptide of SEQ ID NO: 2. The portion is typically at least 50, 100, 150 or 200 nucleotides in length, preferably at least 250, 300, 350 or 400 nucleotides in length, more preferably at least 450, 500, 550, 600 or 650 nucleotides in length.

Preferably, the portion is a portion of a nucleic acid as represented by the sequences listed in Table A. Most preferably the portion is a portion of a nucleic acid as represented by SEQ ID NO: 1.

The terms “fragment”, “fragment of a sequence” or “part of a sequence” “portion” or “portion thereof” mean a truncated sequence of the original sequence referred to. The truncated sequence (nucleic acid or protein sequence) can vary widely in length; the minimum size being a sequence of sufficient size to provide a sequence with at least a comparable function and/or activity of the original sequence referred to or hybidizing with the nucleic acid molecule of the invention or used in the process of the invention under stringend conditions, while the maximum size is not critical. In some applications, the maximum size usually is not substantially greater than that required to provide the desired activity and/or function(s) of the original sequence. A comparable function means at least 40%, 45% or 50%, preferably at least 60%, 70%, 80% or 90% or more of the original sequence.

Another variant of a nucleic acid encoding a HAL3 polypeptide, useful in the methods of the present invention, is a nucleic acid capable of hybridising under reduced stringency conditions, preferably under stringent conditions, with a probe derived from the nucleic acid as defined hereinbefore, which hybridising sequence encodes a polypeptide comprising from N-terminus to C-terminus features (i) a substrate binding helix, (ii) an insertion His motif, (iii) a PXMNXXMW motif and (iv) a substrate recognition clamp; and has in increasing order of preference at least 65%, 70%, 75%, 80%, 85%, 90% or 95% sequence identity to the conserved region represented by SEQ ID NO: 8.

Preferably, the hybridising sequence is one that is capable of hybridising to a nucleic acid as represented by (or to probes derived from) the sequences listed in Table A, or to a portion of any of these sequences (the target sequence). Most preferably the hybridising sequence is capable of hybridising to SEQ ID NO: 1 (or to probes derived therefrom). Probes are generally less than 700 bp or 600 bp in length, preferably less than 500, 400 bp, 300 bp 200 bp or 100 bp in length. Commonly, probe lengths for DNA-DNA hybridisations such as Southern blotting, vary between 100 and 500 bp, whereas the hybridising region in probes for DNA-DNA hybridisations such as in PCR amplification generally are shorter than 50 but longer than 10 nucleotides, preferably they are 15, 20, 25, 30, 35, 40, 45 or 50 bp in length.

The HAL3 polypeptide may be encoded by a splice variant. The term “splice variant” as used herein encompasses variants of a nucleic acid sequence in which selected introns and/or exons have been excised, replaced, displaced or added, or in which introns have been shortened or lengthened. Such variants will be ones in which the substantial biological activity of the protein is retained, which may be achieved by selectively retaining functional segments of the protein. Such splice variants may be found in nature or may be manmade. Methods for making such splice variants are well known in the art.

Preferred splice variants are splice variants of the nucleic acid encoding a HAL3 polypeptide comprising from N-terminus to C-terminus (i) a substrate binding helix, (ii) an insertion His motif, (iii) a PXMNXXMW motif and (iv) a substrate recognition clamp; and having in increasing order of preference at least 65%, 70%, 75%, 80%, 85%, 90% or 95% sequence identity to the conserved region represented by SEQ ID NO: 8.

Further preferred splice variants of nucleic acids encoding HAL3 polypeptides comprising features as defined hereinabove are splice variants of a nucleic acid as represented by any one of the sequences listed in Table A. Most preferred is a splice variant of a nucleic acid sequence as represented by SEQ ID NO: 1.

The HAL3 polypeptide may also be encoded by an allelic variant of a nucleic acid encoding a polypeptide comprising from N-terminus to C-terminus (i) a substrate binding helix, (ii) an insertion His motif, (iii) a PXMNXXMW motif and (iv) a substrate recognition clamp; and having in increasing order of preference at least 65%, 70%, 75%, 80%, 85%, 90% or 95% sequence identity to the conserved region represented by SEQ ID NO: 8.

Preferred allelic variants of nucleic acids encoding HAL3 polypeptides comprising features as defined hereinabove are allelic variants of a nucleic acid as represented by any one of the sequences listed in Table A. Most preferred is an allelic variant of a nucleic acid sequence as represented by SEQ ID NO: 1.

Directed evolution (or gene shuffling) may also be used to generate variants of nucleic acids encoding HAL3 polypeptides. Site-directed mutagenesis may be used to generate variants of nucleic acids encoding HAL3 polypeptides. Several methods are available to achieve site-directed mutagenesis, the most common being PCR based methods (Current Protocols in Molecular Biology. Wiley Eds.).

Nucleic acids encoding HAL3 polypeptides may be derived from any natural or artificial source. The nucleic acid may be modified from its native form in composition and/or genomic environment through deliberate human manipulation. Preferably the HAL3 nucleic acid is from a plant, further preferably from a dicotyledonous plant, more preferably from the family Brassicaceae, most preferably the nucleic acid is from Arabidopsis thaliana.

The increased expression of a nucleic acid encoding a HAL3 polypeptide, preferentially in shoots of a plant, may be performed by introducing a genetic modification (preferably in the locus of a HAL3 gene). The locus of a gene as defined herein is taken to mean a genomic region, which includes the gene of interest and 10 KB up- or downstream of the coding region.

The genetic modification may be introduced, for example, by any one (or more) of the following methods: T-DNA activation, TILLING and homologous recombination (as described in the definitions section) or by introducing and increasing expression a nucleic acid encoding a HAL3 polypeptide preferentially in expanding tissues of a plant. Following introduction of the genetic modification, there follows an optional step of selecting for increased expression of a nucleic acid encoding a HAL3 factor polypeptide preferentially in expanding tissues, which increased expression gives plants having increased yield.

T-DNA activation tagging results in transgenic plants that show dominant phenotypes due to modified expression of genes close to the introduced promoter. The promoter to be introduced may be any promoter capable of increasing expression of the nucleic acid encoding a HAL3 polypeptide preferentially in expanding tissues of a plant.

A genetic modification may also be introduced in the locus of a gene encoding a HAL3 polypeptide using the technique of TILLING (Targeted Induced Local Lesions In Genomes). Plants carrying such mutant variants have increased expression of a nucleic acid encoding a HAL3 polypeptide preferentially in expanding plant tissues.

T-DNA activation and TILLING are examples of technologies that enable the generation of genetic modifications comprising preferentially increasing expression of a nucleic acid encoding a HAL3 polypeptide in expanding tissues of plants.

The effects of the invention may also be reproduced using homologous recombination. The nucleic acid to be targeted is preferably the region controlling the natural expression of a nucleic acid encoding a HAL3 polypeptide in a plant. A weak promoter specific for expression in shoots is introduced into this region, replacing it partly or substantially all of it.

A preferred method for introducing a genetic modification (which in this case need not be in the locus of a HAL3 gene) is to introduce and express preferentially in the shoot of a plant a nucleic acid encoding a HAL3 polypeptide, as defined hereinabove. The nucleic acid to be introduced into a plant may be a full-length nucleic acid or may be a portion or a hybridising sequence or another nucleic acid variant as hereinbefore defined.

The methods of the invention rely on preferentially increased expression of a nucleic acid encoding a HAL3 polypeptide in shoot tissue of a plant, preferably in the cell expansion zone of vegetative shoots.

The invention also provides genetic constructs and vectors to facilitate introduction and/or preferential expression of the nucleic acid sequences useful in the methods according to the invention, in shoots, preferably in expanding tissues of a plant shoots.

Therefore, there is provided a gene construct comprising:

-   -   (i) a nucleic acid encoding a HAL3 polypeptide as defined         hereinabove;     -   (ii) one or more control sequences, of which at least one is a         shoot-specific promoter, operably linked to the nucleic acid of         (i).

Constructs useful in the methods according to the present invention may be constructed using recombinant DNA technology well known to persons skilled in the art. The gene constructs may be inserted into vectors, which may be commercially available, suitable for transforming into plants and suitable for expression of the gene of interest in the transformed cells. The invention therefore provides use of a gene construct as defined hereinabove in the methods of the invention.

Plants are transformed with a vector comprising the sequence of interest (i.e., a nucleic acid encoding a HAL3 polypeptide). The skilled artisan is well aware of the genetic elements that must be present on the vector in order to successfully transform, select and propagate host cells containing the sequence of interest. The sequence of interest is operably linked to one or more control sequences (at least to a promoter).

Suitable promoters, which are functional in plants, are generally known. They may take the form of constitutive or inducible promoters. Suitable promoters can enable the development- and/or tissue-specific expression in multi-celled eukaryotes; thus, leaf-, root-, flower-, seed-, stomata-, tuber- or fruit-specific promoters may advantageously be used in plants.

Different plant promoters usable in plants are promoters such as, for example, the USP, the LegB4-, the DC3 promoter or the ubiquitin promoter from parsley.

For expression in plants, the nucleic acid molecule must, as described above, be linked operably to or comprise a suitable promoter which expresses the gene at the right point in time and in a cell- or tissue-specific manner. Usable promoters are constitutive promoters (Benfey et al., EMBO J. 8 (1989) 2195-2202), such as those which originate from plant viruses, such as 35S CAMV (Franck et al., Cell 21 (1980) 285-294), 19S CaMV (see also U.S. Pat. No. 5,352,605 and WO 84/02913), 34S FMV (Sanger et al., Plant. Mol. Biol., 14, 1990: 433-443), the parsley ubiquitin promoter, or plant promoters such as the Rubisco small subunit promoter described in U.S. Pat. No. 4,962,028 or the plant promoters PRP1 [Ward et al., Plant. Mol. Biol. 22 (1993)], SSU, PGEL1, OCS [Leisner (1988) Proc Natl Acad Sci USA 85(5): 2553-2557], lib4, usp, mas [Comai (1990) Plant Mol Biol 15 (3):373-381], STLS1, ScBV (Schenk (1999) Plant Mol Biol 39(6):1221-1230), B33, SAD1 or SAD2 (flax promoters, Jain et al., Crop Science, 39 (6), 1999: 1696-1701) or nos [Shaw et al. (1984) Nucleic Acids Res. 12(20):7831-7846]. Further examples of constitutive plant promoters are the sugarbeet V-ATPase promoters (WO 01/14572). Examples of synthetic constitutive promoters are the Super promoter (WO 95/14098) and promoters derived from G-boxes (WO 94/12015). If appropriate, chemical inducible promoters may furthermore also be used, compare EP-A 388186, EP-A 335528, WO 97/06268. Stable, constitutive expression of the proteins according to the invention a plant can be advantageous. However, inducible expression of the polypeptide of the invention is advantageous, if a late expression before the harvest is of advantage, as metabolic manipulation may lead to plant growth retardation.

The expression of plant genes can also be facilitated via a chemical inducible promoter (for a review, see Gatz 1997, Annu. Rev. Plant Physiol. Plant Mol. Biol., 48:89-108). Chemically inducible promoters are particularly suitable when it is desired to express the gene in a time-specific manner. Examples of such promoters are a salicylic acid inducible promoter (WO 95/19443), and abscisic acid-inducible promoter (EP 335 528), a tetracyclin-inducible promoter (Gatz et al. (1992) Plant J. 2, 397-404), a cyclohexanol- or ethanol-inducible promoter (WO 93/21334) or others as described herein.

Other suitable promoters are those which react to biotic or abiotic stress conditions, for example the pathogen-induced PRP1 gene promoter (Ward et al., Plant. Mol. Biol. 22 (1993) 361-366), the tomato heat-inducible hsp80 promoter (U.S. Pat. No. 5,187,267), the potato chill-inducible alpha-amylase promoter (WO 96/12814) or the wound-inducible pinll promoter (EP-A-0 375 091) or others as described herein.

Preferred promoters are in particular those which bring gene expression in tissues and organs, in seed cells, such as endosperm cells and cells of the developing embryo. Suitable promoters are the oilseed rape napin gene promoter (U.S. Pat. No. 5,608,152), the Vicia faba USP promoter (Baeumlein et al., Mol Gen Genet, 1991, 225 (3): 459-67), the Arabidopsis oleosin promoter (WO 98/45461), the Phaseolus vulgaris phaseolin promoter (U.S. Pat. No. 5,504,200), the Brassica Bce4 promoter (WO 91/13980), the bean arc5 promoter, the carrot DcG3 promoter, or the Legumin B4 promoter (LeB4; Baeumlein et al., 1992, Plant Journal, 2 (2): 233-9), and promoters which bring about the seed-specific expression in monocotyledonous plants such as maize, barley, wheat, rye, rice and the like. Advantageous seed-specific promoters are the sucrose binding protein promoter (WO 00/26388), the phaseolin promoter and the napin promoter. Suitable promoters which must be considered are the barley Ipt2 or Ipt1 gene promoter (WO 95/15389 and WO 95/23230), and the promoters described in WO 99/16890 (promoters from the barley hordein gene, the rice glutelin gene, the rice oryzin gene, the rice prolamin gene, the wheat gliadin gene, the wheat glutelin gene, the maize zein gene, the oat glutelin gene, the sorghum kasirin gene and the rye secalin gene). Further suitable promoters are Amy32b, Amy 6-6 and Aleurain [U.S. Pat. No. 5,677,474], Bce4 (oilseed rape) [U.S. Pat. No. 5,530,149], glycinin (soya) [EP 571 741], phosphoenolpyruvate carboxylase (soya) [JP 06/62870], ADR12-2 (soya) [WO 98/08962], isocitrate lyase (oilseed rape) [U.S. Pat. No. 5,689,040] or α-amylase (barley) [EP 781 849]. Other promoters which are available for the expression of genes in plants are leaf-specific promoters such as those described in DE-A 19644478 or light-regulated promoters such as, for example, the pea petE promoter.

Further suitable plant promoters are the cytosolic FBPase promoter or the potato ST-LSI promoter (Stockhaus et al., EMBO J. 8, 1989, 2445), the Glycine max phosphoribosylpyrophosphate amidotransferase promoter (GenBank Accession No. U87999) or the node-specific promoter described in EP-A-0 249 676.

In a preferred embodiment, the nucleic acid sequence encoding a HAL3 polypeptide is operably linked to a shoot a shoot specific promoter. A shoot-specific promoter refers to any promoter able to drive expression of the gene of interest in vegetative plant shoot tissues. Preferably, the shoot specific promoter is able to preferentially drive expression of the gene of interest in expanding tissues of vegetative shoots, that is in the cell expansion zone of vegetative shoots. Reference herein to “preferentially” driving expression in the shoot is taken to mean driving expression of any sequence operably linked thereto in the cell expansion zone of vegetative shoots substantially to the exclusion of driving expression elsewhere in the plant, apart from any residual expression due to leaky promoter expression. The shoot-specific promoter may be either a natural or a synthetic promoter.

Preferably, the shoot-specific promoter is a promoter isolated from a beta-expansin gene, such as a rice beta expansin EXBP9 promoter (WO 2004/070039), as represented by SEQ ID NO: 5 or a promoter of similar strength and/or a promoter with a similar expression pattern as the rice beta expansin promoter (i.e. a functionally equivalent promoter).

It should be clear that the applicability of the present invention is not restricted to the nucleic acid encoding a HAL3 polypeptide represented by SEQ ID NO: 1, nor is the applicability of the invention restricted to expression of a nucleic acid encoding a HAL3 polypeptide when driven by a beta expansin promoter.

Optionally, one or more terminator sequences (also a control sequence) may be used in the construct introduced into a plant. Additional regulatory elements may include transcriptional as well as translational enhancers. Those skilled in the art will be aware of terminator and enhancer sequences that may be suitable for use in performing the invention. Such sequences would be known or may readily be obtained by a person skilled in the art.

The genetic constructs of the invention may further include an origin of replication sequence that is required for maintenance and/or replication in a specific cell type. One example is when a genetic construct is required to be maintained in a bacterial cell as an episomal genetic element (e.g. plasmid or cosmid molecule). Preferred origins of replication include, but are not limited to, the f1-ori and colE1.

Other control sequences (besides promoter, enhancer, silencer, intron sequences, 3′UTR and/or 5′UTR regions) may be protein and/or RNA stabilizing elements.

For the detection and/or selection of the successful transfer of the nucleic acid sequences as depicted in the sequence protocol and used in the process of the invention, it is advantageous to use marker genes (=reporter genes). These marker genes enable the identification of a successful transfer of the nucleic acid molecules via a series of different principles, for example via visual identification with the aid of fluorescence, luminescence or in the wavelength range of light which is discernible for the human eye, by a resistance to herbicides or antibiotics, via what are known as nutritive markers (auxotrophism markers) or antinutritive markers, via enzyme assays or via phytohormones. Examples of such markers which may be mentioned are GFP (=green fluorescent protein); the luciferin/luceferase system, the β-galactosidase with its colored substrates, for example X-Gal, the herbicide resistances to, for example, imidazolinone, glyphosate, phosphinothricin or sulfonylurea, the antibiotic resistances to, for example, bleomycin, hygromycin, streptomycin, kanamycin, tetracyclin, chloramphenicol, ampicillin, gentamycin, geneticin (G418), spectinomycin or blasticidin, to mention only a few, nutritive markers such as the utilization of mannose or xylose, or antinutritive markers such as the resistance to 2-deoxyglucose. This list is a small number of possible markers. The skilled worker is very familiar with such markers. Different markers are preferred, depending on the organism and the selection method.

The present invention also encompasses plants obtainable by the methods according to the present invention. The present invention therefore provides plants, plant parts or plant cells thereof obtainable by the method according to the present invention, which plants or parts or cells thereof comprise a nucleic acid transgene encoding a HAL3 polypeptide under the control of a shoot-specific promoter.

The invention also provides a method for the production of transgenic plants having increased yield relative to control plants, comprising introduction and preferential expression of a nucleic acid encoding a HAL3 polypeptide in the shoot of a plant.

Host plants for the nucleic acids or the vector used in the method according to the invention, the expression cassette or construct or vector are, in principle, advantageously all plants, which are capable of synthesizing the polypeptides used in the inventive method.

More specifically, the present invention provides a method for the production of transgenic plants having increased yield which method comprises:

-   -   (i) introducing and preferentially expressing a nucleic acid         encoding a HAL3 polypeptide in the shoot of a plant; and     -   (ii) cultivating the plant cell under conditions promoting plant         growth and development.

The nucleic acid may be introduced directly into a plant cell or into the plant itself (including introduction into a tissue, organ or any other part of a plant). According to a preferred feature of the present invention, the nucleic acid is preferably introduced into a plant by transformation.

The transfer of foreign genes into the genome of a plant is called transformation. In doing this the methods described for the transformation and regeneration of plants from plant tissues or plant cells are utilized for transient or stable transformation. To select transformed plants, the plant material obtained in the transformation is, as a rule, subjected to selective conditions so that transformed plants can be distinguished from untransformed plants. For example, the seeds obtained in the above-described manner can be planted and, after an initial growing period, subjected to a suitable selection by spraying. A further possibility consists in growing the seeds, if appropriate after sterilization, on agar plates using a suitable selection agent so that only the transformed seeds can grow into plants. Further advantageous transformation methods, in particular for plants, are known to the skilled worker and are described herein below.

Generally after transformation, plant cells or cell groupings are selected for the presence of one or more markers which are encoded by plant-expressible genes co-transferred with the gene of interest, following which the transformed material is regenerated into a whole plant.

As mentioned Agrobacteria transformed with an expression vector according to the invention may also be used in the manner known per se for the transformation of plants such as experimental plants like Arabidopsis or crop plants, such as, for example, cereals, maize, oats, rye, barley, wheat, soya, rice, cotton, sugarbeet, canola, sunflower, flax, hemp, potato, tobacco, tomato, carrot, bell peppers, oilseed rape, tapioca, cassava, arrow root, tagetes, alfalfa, lettuce and the various tree, nut, and grapevine species, in particular oil-containing crop plants such as soya, peanut, castor-oil plant, sunflower, maize, cotton, flax, oilseed rape, coconut, oil palm, safflower (Carthamus tinctorius) or cocoa beans, for example by bathing scarified leaves or leaf segments in an agrobacterial solution and subsequently growing them in suitable media.

In addition to the transformation of somatic cells, which then has to be regenerated into intact plants, it is also possible to transform the cells of plant meristems and in particular those cells which develop into gametes. In this case, the transformed gametes follow the natural plant development, giving rise to transgenic plants. Thus, for example, seeds of Arabidopsis are treated with agrobacteria and seeds are obtained from the developing plants of which a certain proportion is transformed and thus transgenic [Feldman, K A and Marks M D (1987). Mol Gen Genet. 208:274-289; Feldmann K (1992). In: C Koncz, N-H Chua and J Shell, eds, Methods in Arabidopsis Research. Word Scientific, Singapore, pp. 274-289]. Alternative methods are based on the repeated removal of the influorescences and incubation of the excision site in the center of the rosette with transformed agrobacteria, whereby transformed seeds can likewise be obtained at a later point in time (Chang (1994). Plant J. 5: 551-558; Katavic (1994). Mol Gen Genet, 245: 363-370). However, an especially effective method is the vacuum infiltration method with its modifications such as the “floral dip” method. In the case of vacuum infiltration of Arabidopsis, intact plants under reduced pressure are treated with an agrobacterial suspension [Bechthold, N (1993). C R Acad Sci Paris Life Sci, 316: 1194-1199], while in the case of the “floral dip” method the developing floral tissue is incubated briefly with a surfactant-treated agrobacterial suspension [Clough, S J and Bent, A F (1998). The Plant J. 16, 735-743]. A certain proportion of transgenic seeds are harvested in both cases, and these seeds can be distinguished from nontransgenic seeds by growing under the above-described selective conditions. In addition the stable transformation of plastids is of advantages because plastids are inherited maternally is most crops reducing or eliminating the risk of transgene flow through pollen. The transformation of the chloroplast genome is generally achieved by a process, which has been schematically displayed in Klaus et al., 2004 [Nature Biotechnology 22 (2), 225-229]. Briefly the sequences to be transformed are cloned together with a selectable marker gene between flanking sequences homologous to the chloroplast genome. These homologous flanking sequences direct site specific integration into the plastome. Plastidal transformation has been described for many different plant species and an overview can be taken from Bock (2001) Transgenic plastids in basic research and plant biotechnology. J Mol Biol. 2001 Sep. 21; 312 (3):425-38 or Maliga, P (2003) Progress towards commercialization of plastid transformation technology. Trends Biotechnol. 21, 20-28. Further biotechnological progress has recently been reported in form of marker free plastid transformants, which can be produced by a transient cointegrated maker gene (Klaus et al., 2004, Nature Biotechnology 22(2), 225-229).

The genetically modified plant cells can be regenerated via all methods with which the skilled worker is familiar. Suitable methods can be found in the abovementioned publications by S. D. Kung and R. Wu, Potrykus or Höfgen and Willmitzer.

Following DNA transfer and regeneration, putatively transformed plants may be evaluated, for instance using Southern analysis, for the presence of the gene of interest, copy number and/or genomic organisation. Alternatively or additionally, expression levels of the newly introduced DNA may be monitored using Northern and/or Western analysis, or quantitative PCR, all techniques being well known to persons having ordinary skill in the art.

The generated transformed plants may be propagated by a variety of means, such as by clonal propagation or classical breeding techniques. For example, a first generation (or T1) transformed plant may be selfed to give homozygous second generation (or T2) transformants, and the T2 plants further propagated through classical breeding techniques.

The generated transformed organisms may take a variety of forms. For example, they may be chimeras of transformed cells and non-transformed cells; clonal transformants (e.g., all cells transformed to contain the expression cassette); grafts of transformed and untransformed tissues (e.g., in plants, a transformed rootstock grafted to an untransformed scion).

The present invention clearly extends to any plant cell or plant produced by any of the methods described herein, and to all plant parts and propagules thereof. The present invention extends further to encompass the progeny of a primary transformed or transfected cell, tissue, organ or whole plant that has been produced by any of the aforementioned methods, the only requirement being that progeny exhibit the same genotypic and/or phenotypic characteristic(s) as those produced by the parent in the methods according to the invention.

The invention also includes host cells containing an isolated nucleic acid encoding a HAL3 polypeptide. Preferred host cells according to the invention are plant cells.

The invention also extends to harvestable parts of a plant such as, but not limited to seeds, leaves, fruits, flowers, stems, rhizomes, tubers and bulbs. The invention furthermore relates to products derived, preferably directly derived, from a harvestable part of such a plant, such as dry pellets or powders, oil, fat and fatty acids, starch or proteins.

The present invention also encompasses use of nucleic acids encoding HAL3 polypeptides and use of HAL3 polypeptides in increasing plant yield as defined hereinabove in the methods of the invention.

Nucleic acids encoding HAL3 polypeptides, or HAL3 polypeptides, may find use in breeding programmes in which a DNA marker is identified which may be genetically linked to a HAL3 gene. The nucleic acids/genes, or the HAL3 polypeptides may be used to define a molecular marker. This DNA or protein marker may then be used in breeding programmes to select plants having increased yield as defined hereinabove in the methods of the invention.

Allelic variants of a HAL3 nucleic acid/gene may also find use in marker-assisted breeding programmes. Such breeding programmes sometimes require introduction of allelic variation by mutagenic treatment of the plants, using for example EMS mutagenesis; alternatively, the programme may start with a collection of allelic variants of so called “natural” origin caused unintentionally. Identification of allelic variants then takes place, for example, by PCR. This is followed by a step for selection of superior allelic variants of the sequence in question and which give increased yield. Selection is typically carried out by monitoring growth performance of plants containing different allelic variants of the sequence in question. Growth performance may be monitored in a greenhouse or in the field. Further optional steps include crossing plants in which the superior allelic variant was identified with another plant. This could be used, for example, to make a combination of interesting phenotypic features.

A nucleic acid encoding a HAL3 polypeptide may also be used as probes for genetically and physically mapping the genes that they are a part of, and as markers for traits linked to those genes. Such information may be useful in plant breeding in order to develop lines with desired phenotypes. Such use of HAL3 nucleic acids requires only a nucleic acid sequence of at least 15 nucleotides in length. The HAL3 nucleic acids may be used as restriction fragment length polymorphism (RFLP) markers. Southern blots (Sambrook J, Fritsch E F and Maniatis T (1989) Molecular Cloning, A Laboratory Manual) of restriction-digested plant genomic DNA may be probed with the HAL3 nucleic acids. The resulting banding patterns may then be subjected to genetic analyses using computer programs such as MapMaker (Lander et al. (1987) Genomics 1: 174-181) in order to construct a genetic map. In addition, the nucleic acids may be used to probe Southern blots containing restriction endonuclease-treated genomic DNAs of a set of individuals representing parent and progeny of a defined genetic cross. Segregation of the DNA polymorphisms is noted and used to calculate the position of the HAL3 nucleic acid in the genetic map previously obtained using this population (Botstein et al. (1980) Am. J. Hum. Genet. 32:314-331).

The production and use of plant gene-derived probes for use in genetic mapping is described in Bernatzky and Tanksley (1986) Plant Mol. Biol. Reporter 4: 37-41. Numerous publications describe genetic mapping of specific cDNA clones using the methodology outlined above or variations thereof. For example, F2 intercross populations, backcross populations, randomly mated populations, near isogenic lines, and other sets of individuals may be used for mapping. Such methodologies are well known to those skilled in the art.

The nucleic acid probes may also be used for physical mapping (i.e., placement of sequences on physical maps; see Hoheisel et al. In: Non-mammalian Genomic Analysis: A Practical Guide, Academic press 1996, pp. 319-346, and references cited therein).

In another embodiment, the nucleic acid probes may be used in direct fluorescence in situ hybridisation (FISH) mapping (Trask (1991) Trends Genet. 7:149-154). Although current methods of FISH mapping favour use of large clones (several kb to several hundred kb; see Laan et al. (1995) Genome Res. 5:13-20), improvements in sensitivity may allow performance of FISH mapping using shorter probes.

A variety of nucleic acid amplification-based methods for genetic and physical mapping may be carried out using the nucleic acids. Examples include allele-specific amplification (Kazazian (1989) J. Lab. Clin. Med. 11:95-96), polymorphism of PCR-amplified fragments (CAPS; Sheffield et al. (1993) Genomics 16:325-332), allele-specific ligation (Landegren et al. (1988) Science 241:1077-1080), nucleotide extension reactions (Sokolov (1990) Nucleic Acid Res. 18:3671), Radiation Hybrid Mapping (Walter et al. (1997) Nat. Genet. 7:22-28) and Happy Mapping (Dear and Cook (1989) Nucleic Acid Res. 17:6795-6807). For these methods, the sequence of a nucleic acid is used to design and produce primer pairs for use in the amplification reaction or in primer extension reactions. The design of such primers is well known to those skilled in the art. In methods employing PCR-based genetic mapping, it may be necessary to identify DNA sequence differences between the parents of the mapping cross in the region corresponding to the instant nucleic acid sequence. This, however, is generally not necessary for mapping methods.

The methods according to the present invention result in plants having increased yield, as described hereinbefore. This increased yield may also be combined with other economically advantageous traits, such as further yield-enhancing traits, tolerance to other abiotic and biotic stresses, traits modifying various architectural features and/or biochemical and/or physiological features.

Detailed Description for MADS15 Up

Surprisingly, it has now been found that modulating expression in a plant of a nucleic acid encoding a MADS15 polypeptide gives plants having enhanced yield-related traits relative to control plants. The particular class of MADS15 polypeptides suitable for enhancing yield-related traits in plants is described in detail below.

The present invention provides a method for enhancing yield-related traits in plants relative to control plants, comprising modulating expression in a plant of a nucleic acid encoding a MADS15 polypeptide.

Any reference hereinafter to a “protein useful in the methods of the invention” is taken to mean a MADS15 polypeptide as defined herein. Any reference hereinafter to a “nucleic acid useful in the methods of the invention” is taken to mean a nucleic acid capable of encoding such a MADS15 polypeptide.

A preferred method for modulating (preferably, increasing) expression of a nucleic acid encoding a protein useful in the methods of the invention is by introducing and expressing in a plant a nucleic acid encoding a protein useful in the methods of the invention as defined below.

The nucleic acid to be introduced into a plant (and therefore useful in performing the methods of the invention) is any nucleic acid encoding the type of protein which will now be described, hereafter also named “MADS15 nucleic acid” or “MADS15 gene”.

The term “MADS15 polypeptide” as defined herein refers to a protein that falls in the group of FUL-like MADS box proteins as delineated by Adam et al. (J. Mol. Evol. 62, 15-31). FUL-like MADS box proteins are part of the SQUAMOSA subfamily and have the typical MIKC^(c) architecture: a MADS domain (M) at the N-terminus, followed by an intervening domain (I) involved in dimerisation, a highly conserved keratin domain (K) and a variable domain (C) at the C-terminus, which is responsible for binding of interacting proteins or transcriptional activation (De Bodt et al. Trends in Plant Science 8, 475-483).

Plant MADS15 polypeptides may also be identified by the presence of certain conserved motifs. The presence of these conserved motifs may be identified using methods for the alignment of sequences for comparison as described hereinabove. In some instances, the default parameters may be adjusted to modify the stringency of the search. For example using BLAST, the statistical significance threshold (called “expect” value) for reporting matches against database sequences may be increased to show less stringent matches. This way, short nearly exact matches may be identified. Upon identification of a MADS15 polypeptide by the presence of these motifs, a person skilled in the art may easily derive the corresponding nucleic acid encoding the polypeptide comprising the relevant motifs, and use a sufficient length of contiguous nucleotides of the same to perform any one or more of the gene silencing methods described above (for the reduction or substantial elimination of an endogenous MADS15 gene expression).

Typically, the presence of at least one of the motifs 1 to 4 should be sufficient to identify any query sequence as a MADS15, however, the presence of at least motifs 1 and 2 is preferred. The consensus sequence provided is based on the monocot sequences given in the sequence listing. A person skilled in the art would be well aware that the consensus sequence may vary somewhat if further or different sequences (for example from dicotyledonous plants) were used for comparison.

Motif 1, located in the MADS domain (SEQ ID NO: 48):

L(L/V)KKA(H/N)EIS(VI)L(C/Y)DAE(V/I/L) (A/G) (L/A/V) (I/V) (I/V)FS(T/P/A/N)KGKLYE(Y/F) (A/S) (T/S)(D/N/E)S(K/C/R/S)M(D/E) (N/I/R/K)IL(E/D)R.

Preferably, this conserved sequence motif 1 has the sequence:

LLKKAHEISVLCDAEVA (L/A/V)I(I/V)FS(T/P)KGKLYEYATDS (C/R)M(D/E)(R/K)ILER, most preferably the conserved sequence motif 1 has the sequence:

LLKKAHEISVLCDAEVAAIVFSPKGKLYEYATDSRMDKILER

Motif 2, located in the K domain (SEQ ID NO: 49):

KLK(A/S) (K/R) (V/I)E(A/T/S) (L/I) (Q/N) (K/R/N) (S/C/R) (Q/H) (R/K)HLMGE

Preferably, this conserved sequence motif 2 has the sequence:

KLKAK(V/I)E(A/T) (L/I)QK(S/C) (Q/H) (R/K)HLMGE

More preferably, this conserved sequence motif 2 has the sequence:

KLKAKIETIQKCHKHLMGE

Optionally, the MADS15 polypeptide or its homologue may comprise in the C domain motif 3 and/or motif 4:

motif 3 (SEQ ID NO: 50): Q(P/Q/V/A)QTS (S/F) (S/F) (S/F) (S/F) (S/C/F) (F/M) motif 4 (SEQ ID NO: 51): (G/A/V/L) (L/P)XWMX(S/H) wherein the first X residue in motif 4 may be any amino acid, but preferably L, P or H; and wherein the second X residue may be any amino acid, but preferably V or L.

Alternatively, the C-domain (starting behind the keratin domain, i.e. at R175 in SEQ ID NO: 44) may be characterised by the increased occurrence of glutamine (normally 3.93%, here at least 8.77% with a maximum of 26.73%), in addition, the content in alanine, proline, and/or serine may also be increased (above 7.8%, 4.85% and 6.89% respectively).

Alternatively formulated, a preferred MADS15 protein useful in the methods of the present invention comprises at least an N-terminal MADS domain corresponding to the SMART domain SM00432 (Pfam PF00319) followed by a Keratin domain corresponding to the K-box region defined in Pfam as PF01486, more preferably, the MADS15 protein has in its MADS domain the conserved signature of SEQ ID NO: 48 and in its K-domain the conserved signature of SEQ ID NO: 49, most preferably, the MADS15 protein has the sequence given in SEQ ID NO: 44.

Examples of proteins useful in the methods of the invention and nucleic acids encoding the same are given below in table D of Example 8.

Also useful in the methods of the invention are homologues of any one of the amino acid sequences given in table D.

Also useful in the methods of the invention are derivatives of any one of the polypeptides given in table D or orthologues or paralogues of any of the aforementioned SEQ ID NOs. A preferred derivative is a derivative of SEQ ID NO: 44. Derivatives of the polypeptides given in table D are further examples which may be suitable for use in the methods of the invention. Derivatives useful in the methods of the present invention preferably have similar biological and functional activity as the unmodified protein from which they are derived.

The invention is illustrated by transforming plants with the Oryza sativa nucleic acid sequence represented by SEQ ID NO: 43, encoding the polypeptide sequence of SEQ ID NO: 44, however performance of the invention is not restricted to these sequences. The methods of the invention may advantageously be performed using any nucleic acid encoding a protein useful in the methods of the invention as defined herein, including orthologues and paralogues, such as any of the nucleic acid sequences given in table D. The amino acid sequences given in table D may be considered to be orthologues and paralogues of the MADS15 polypeptide represented by SEQ ID NO: 44.

Orthologues and paralogues may easily be found by performing a so-called reciprocal blast search. Typically, this involves a first BLAST involving BLASTing a query sequence (for example using any of the sequences listed in table D) against any sequence database, such as the publicly available NCBI database. BLASTN or TBLASTX (using standard default values) are generally used when starting from a nucleotide sequence, and BLASTP or TBLASTN (using standard default values) when starting from a protein sequence. The BLAST results may optionally be filtered. The full-length sequences of either the filtered results or non-filtered results are then BLASTed back (second BLAST) against sequences from the organism from which the query sequence is derived (where the query sequence is SEQ ID NO: 43 or SEQ ID NO: 44, the second BLAST would therefore be against Oryza sativa sequences). The results of the first and second BLASTs are then compared. A paralogue is identified if a high-ranking hit from the first blast is from the same species as from which the query sequence is derived, a BLAST back then ideally results in the query sequence as highest hit; an orthologue is identified if a high-ranking hit in the first BLAST is not from the same species as from which the query sequence is derived, and preferably results upon BLAST back in the query sequence being among the highest hits.

High-ranking hits are those having a low E-value. The lower the E-value, the more significant the score (or in other words the lower the chance that the hit was found by chance). Computation of the E-value is well known in the art. In addition to E-values, comparisons are also scored by percentage identity. Percentage identity refers to the number of identical nucleotides (or amino acids) between the two compared nucleic acid (or polypeptide) sequences over a particular length. In the case of large families, ClustalW may be used, followed by a neighbour joining tree, to help visualize clustering of related genes and to identify orthologues and paralogues.

Table D gives examples of orthologues and paralogues of the MADS15 protein represented by SEQ ID NO 44. Further orthologues and paralogues may readily be identified using the BLAST procedure described above.

The proteins of the invention are identifiable by the presence of the conserved MADS and/or keratin domain(s) (shown in FIG. 5). Specialist databases exist for the identification of domains, for example, SMART (Schultz et al. (1998) Proc. Natl. Acad. Sci. USA 95, 5857-5864; Letunic et al. (2002) Nucleic Acids Res 30, 242-244, InterPro (Mulder et al., (2003) Nucl. Acids. Res. 31, 315-318, Prosite (Bucher and Bairoch (1994), A generalized profile syntax for biomolecular sequences motifs and its function in automatic sequence interpretation. (In) ISMB-94; Proceedings 2nd International Conference on Intelligent Systems for Molecular Biology. Altman R., Brutlag D., Karp P., Lathrop R., Searls D., Eds., pp 53-61, AAAIPress, Menlo Park; Hulo et al., Nucl. Acids. Res. 32:D134-D137, (2004), or Pfam (Bateman et al., Nucleic Acids Research 30(1): 276-280 (2002). A set of tools for in silico analysis of protein sequences is available on the ExPASY proteomics server (hosted by the Swiss Institute of Bioinformatics (Gasteiger et al., ExPASy: the proteomics server for in-depth protein knowledge and analysis, Nucleic Acids Res. 31:3784-3788 (2003)).

Domains may also be identified using routine techniques, such as by sequence alignment. Methods for the alignment of sequences for comparison are well known in the art, such methods include GAP, BESTFIT, BLAST, FASTA and TFASTA. GAP uses the algorithm of Needleman and Wunsch ((1970) J Mol Biol 48: 443-453) to find the global (i.e. spanning the complete sequences) alignment of two sequences that maximizes the number of matches and minimizes the number of gaps. The BLAST algorithm (Altschul et al. (1990) J Mol Biol 215: 403-10) calculates percent sequence identity and performs a statistical analysis of the similarity between the two sequences. The software for performing BLAST analysis is publicly available through the National Centre for Biotechnology Information (NCBI). Homologues may readily be identified using, for example, the ClustalW multiple sequence alignment algorithm (version 1.83), with the default pairwise alignment parameters, and a scoring method in percentage. Global percentages of similarity and identity may also be determined using one of the methods available in the MatGAT software package (Campanella et al., BMC Bioinformatics. 2003 Jul. 10; 4:29. MatGAT: an application that generates similarity/identity matrices using protein or DNA sequences.). Minor manual editing may be performed to optimise alignment between conserved motifs, as would be apparent to a person skilled in the art. Furthermore, instead of using full-length sequences for the identification of homologues, specific domains (such as the MADS or keratin domain, or one of the motifs defined above) may be used as well. The sequence identity values, which are indicated below in Example 10 as a percentage were determined over the entire nucleic acid or amino acid sequence, and/or over selected domains or conserved motif(s), using the programs mentioned above using the default parameters.

Furthermore, a MADS15 protein may also be identifiable by its ability or inability to bind DNA and to interact with other proteins. DNA-binding activity and protein-protein interactions may readily be determined in vitro or in vivo using techniques well known in the art. Examples of in vitro assays for DNA binding activity include: gel retardation analysis using known MADS-box DNA binding domains (West et al. (1998) Nucl Acid Res 26(23): 5277-87), or yeast one-hybrid assays. An example of an in vitro assay for protein-protein interactions is the yeast two-hybrid analysis (Fields and Song (1989) Nature 340:245-6). Proteins known to interact with OsMADS15 include other MADS proteins (such as those involved in the flowering signalling complex), receptor like kinases such a Clavata1 and Clavata2, Erecta, BRI1 or RSK. Further details are provided in Example 13.

Nucleic acids encoding proteins useful in the methods of the invention need not be full-length nucleic acids, since performance of the methods of the invention does not rely on the use of full-length nucleic acid sequences. Examples of nucleic acids suitable for use in performing the methods of the invention include the nucleic acid sequences given in table D, but are not limited to those sequences. Nucleic acid variants may also be useful in practising the methods of the invention. Examples of such nucleic acid variants include portions of nucleic acids encoding a protein useful in the methods of the invention, nucleic acids hybridising to nucleic acids encoding a protein useful in the methods of the invention, splice variants of nucleic acids encoding a protein useful in the methods of the invention, allelic variants of nucleic acids encoding a protein useful in the methods of the invention and variants of nucleic acids encoding a protein useful in the methods of the invention that are obtained by gene shuffling. The terms portion, hybridising sequence, splice variant, allelic variant and gene shuffling will now be described.

According to the present invention, there is provided a method for enhancing yield-related traits in plants, comprising introducing and expressing in a plant a portion of any one of the nucleic acid sequences given in table D, or a portion of a nucleic acid encoding an orthologue, paralogue or homologue of any of the amino acid sequences given in table D.

Portions useful in the methods of the invention, encode a polypeptide falling within the definition of a nucleic acid encoding a protein useful in the methods of the invention as defined herein and having substantially the same biological activity as the amino acid sequences given in table D. Preferably, the portion is a portion of any one of the nucleic acids given in table D. The portion is typically at least 400 consecutive nucleotides in length, preferably at least 600 consecutive nucleotides in length, more preferably at least 700 consecutive nucleotides in length and most preferably at least 800 consecutive nucleotides in length, the consecutive nucleotides being of any one of the nucleic acid sequences given in table D. Most preferably the portion is a portion of the nucleic acid of SEQ ID NO: 43. Preferably, the portion encodes an amino acid sequence comprising (any one or more of) the MADS and keratin domain as defined herein.

A portion of a nucleic acid encoding a MADS15 protein as defined herein may be prepared, for example, by making one or more deletions to the nucleic acid. The portions may be used in isolated form or they may be fused to other coding (or non coding) sequences in order to, for example, produce a protein that combines several activities. When fused to other coding sequences, the resultant polypeptide produced upon translation may be bigger than that predicted for the MADS15 protein portion.

Another nucleic acid variant useful in the methods of the invention is a nucleic acid capable of hybridising, under reduced stringency conditions, preferably under stringent conditions, with a nucleic acid encoding a MADS15 protein as defined herein, or with a portion as defined herein.

Hybridising sequences useful in the methods of the invention, encode a polypeptide having a MADS and/or keratin domain (see the alignment of FIG. 6) and having substantially the same biological activity as the MADS15 protein represented by any of the amino acid sequences given in table D. The hybridising sequence is typically at least 400 consecutive nucleotides in length, preferably at least 600 consecutive nucleotides in length, more preferably at least 700 consecutive nucleotides in length and most preferably at least 800 consecutive nucleotides in length, the consecutive nucleotides being of any one of the nucleic acid sequences given in table D. Preferably, the hybridising sequence is one that is capable of hybridising to any of the nucleic acids given in table D, or to a portion of any of these sequences, a portion being as defined above. Most preferably, the hybridising sequence is capable of hybridising to a nucleic acid as represented by SEQ ID NO: 43 or to a portion thereof. Preferably, the hybridising sequence encodes an amino acid sequence comprising any one or more of the motifs or domains as defined herein.

According to the present invention, there is provided a method for enhancing yield-related traits in plants, comprising introducing and expressing in a plant a nucleic acid capable of hybridizing to any one of the nucleic acids given in table D, or comprising introducing and expressing in a plant a nucleic acid capable of hybridising to a nucleic acid encoding an orthologue, paralogue or homologue of any of the nucleic acid sequences given in table D.

Another nucleic acid variant useful in the methods of the invention is a splice variant encoding a MADS15 protein as defined hereinabove.

According to the present invention, there is provided a method for enhancing yield-related traits in plants, comprising introducing and expressing in a plant a splice variant of any one of the nucleic acid sequences given in table D, or a splice variant of a nucleic acid encoding an orthologue, paralogue or homologue of any of the amino acid sequences given in table D.

Preferred splice variants are splice variants of a nucleic acid represented by SEQ ID NO: 43 or a splice variant of a nucleic acid encoding an orthologue or paralogue of SEQ ID NO: 44. Preferably, the amino acid sequence encoded by the splice variant comprises any one or more of the motifs or domains as defined herein.

Another nucleic acid variant useful in performing the methods of the invention is an allelic variant of a nucleic acid encoding a MADS15 protein as defined hereinabove. The allelic variants useful in the methods of the present invention have substantially the same biological activity as the MADS15 protein of SEQ ID NO: 44.

According to the present invention, there is provided a method for enhancing yield-related traits in plants, comprising introducing and expressing in a plant an allelic variant of any one of the nucleic acids given in table D, or comprising introducing and expressing in a plant an allelic variant of a nucleic acid encoding an orthologue, paralogue or homologue of any of the amino acid sequences given in table D.

Preferably, the allelic variant is an allelic variant of SEQ ID NO: 43 or an allelic variant of a nucleic acid encoding an orthologue or paralogue of SEQ ID NO: 44. Preferably, the amino acid sequence encoded by the allelic variant comprises any one or more of the motifs or domains as defined herein.

A further nucleic acid variant useful in the methods of the invention is a nucleic acid variant obtained by gene shuffling. Gene shuffling or directed evolution may also be used to generate variants of nucleic acids encoding MADS15 proteins as defined above.

According to the present invention, there is provided a method for enhancing yield-related traits in plants, comprising introducing and expressing in a plant a variant of any one of the nucleic acid sequences given in table D, or comprising introducing and expressing in a plant a variant of a nucleic acid encoding an orthologue, paralogue or homologue of any of the amino acid sequences given in table D, which variant nucleic acid is obtained by gene shuffling.

Preferably, the variant nucleic acid obtained by gene shuffling encodes an amino acid sequence comprising any one or more of the motifs or domains as defined herein.

Furthermore, nucleic acid variants may also be obtained by site-directed mutagenesis. Several methods are available to achieve site-directed mutagenesis, the most common being PCR based methods (Current Protocols in Molecular Biology. Wiley Eds.).

Nucleic acids encoding MADS15 proteins may be derived from any natural or artificial source. The nucleic acid may be modified from its native form in composition and/or genomic environment through deliberate human manipulation. Preferably the MADS15-encoding nucleic acid is from a plant, further preferably from a monocotyledonous plant, more preferably from the Poaceae family, most preferably the nucleic acid is from Oryza sativa.

Any reference herein to a MADS15 protein is therefore taken to mean a MADS15 protein as defined above. Any nucleic acid encoding such a MADS15 protein is suitable for use in performing the methods of the invention.

The present invention also encompasses plants or parts thereof (including seeds) obtainable by the methods according to the present invention. The plants or parts thereof comprise a nucleic acid transgene encoding a MADS15 protein as defined above.

The invention also provides genetic constructs and vectors to facilitate introduction and/or expression of the nucleic acid sequences useful in the methods according to the invention, in a plant. The gene constructs may be inserted into vectors, which may be commercially available, suitable for transforming into plants and suitable for expression of the gene of interest in the transformed cells. The invention also provides use of a gene construct as defined herein in the methods of the invention.

More specifically, the present invention provides a construct comprising

-   -   (a) nucleic acid encoding MADS15 protein as defined above;     -   (b) one or more control sequences capable of driving expression         of the nucleic acid sequence of (a); and optionally     -   (c) a transcription termination sequence.

Plants are transformed with a vector comprising the sequence of interest (i.e., a nucleic acid encoding a MADS15 polypeptide as defined herein. The skilled artisan is well aware of the genetic elements that must be present on the vector in order to successfully transform, select and propagate host cells containing the sequence of interest. The sequence of interest is operably linked to one or more control sequences (at least to a promoter).

Advantageously, any type of promoter may be used to drive expression of the nucleic acid sequence.

The promoter may be a constitutive promoter; alternatively, the promoter may be an inducible promoter, i.e. having induced or increased transcription initiation in response to a chemical or a stress-inducible promoter, or a pathogen-induced promoter.

Additionally or alternatively, the promoter may be an organ-specific or tissue-specific promoter, or the promoter may be a ubiquitous promoter, or the promoter may be developmentally regulated. Furthermore, the promoter may be organ-specific or tissue-specific or cell-specific.

Preferably, the MADS15 nucleic acid or variant thereof is operably linked to a constitutive promoter. A preferred constitutive promoter is one that is also substantially ubiquitously expressed. Further preferably the promoter is derived from a plant, more preferably a monocotyledonous plant. Most preferred is use of a GOS2 promoter (for example from rice, SEQ ID NO: 47 or SEQ ID NO: 108). It should be clear that the applicability of the present invention is not restricted to the MADS15 nucleic acid represented by SEQ ID NO: 43, nor is the applicability of the invention restricted to expression of a MADS15 nucleic acid when driven by a GOS2 promoter. Examples of other constitutive promoters or functionally equivalent promters which may also be used to drive expression of a MADS15 nucleic acid are shown in the definitions section.

Optionally, one or more terminator sequences may be used in the construct introduced into a plant. Additional regulatory elements may include transcriptional as well as translational enhancers. Those skilled in the art will be aware of terminator and enhancer sequences that may be suitable for use in performing the invention. Such sequences would be known or may readily be obtained by a person skilled in the art.

An intron sequence may also be added to the 5′ untranslated region (UTR) or in the coding sequence to increase the amount of the mature message that accumulates in the cytosol.

Other control sequences (besides promoter, enhancer, silencer, intron sequences, 3′UTR and/or 5′UTR regions) may be protein and/or RNA stabilizing elements. Such sequences would be known or may readily be obtained by a person skilled in the art.

The genetic constructs of the invention may further include an origin of replication sequence that is required for maintenance and/or replication in a specific cell type. One example is when a genetic construct is required to be maintained in a bacterial cell as an episomal genetic element (e.g. plasmid or cosmid molecule). Preferred origins of replication include, but are not limited to, the f1-ori and colE1.

For the detection of the successful transfer of the nucleic acid sequences as used in the methods of the invention and/or selection of transgenic plants comprising these nucleic acids, it is advantageous to use marker genes (or reporter genes). Therefore, the genetic construct may optionally comprise a selectable marker gene.

The invention also provides a method for the production of transgenic plants having enhanced yield-related traits relative to control plants, comprising introduction and expression in a plant of any nucleic acid encoding a MADS15 protein as defined hereinabove.

More specifically, the present invention provides a method for the production of transgenic plants having increased yield, which method comprises:

-   -   (i) introducing and expressing in a plant or plant cell a MADS15         nucleic acid or variant thereof; and     -   (ii) cultivating the plant cell under conditions promoting plant         growth and development.

The nucleic acid may be introduced directly into a plant cell or into the plant itself (including introduction into a tissue, organ or any other part of a plant). According to a preferred feature of the present invention, the nucleic acid is preferably introduced into a plant by transformation.

The genetically modified plant cells can be regenerated via all methods with which the skilled worker is familiar. Suitable methods can be found in the abovementioned publications by S. D. Kung and R. Wu, Potrykus or Hofgen and Willmitzer.

Generally after transformation, plant cells or cell groupings are selected for the presence of one or more markers which are encoded by plant-expressible genes co-transferred with the gene of interest, following which the transformed material is regenerated into a whole plant. To select transformed plants, the plant material obtained in the transformation is, as a rule, subjected to selective conditions so that transformed plants can be distinguished from untransformed plants. For example, the seeds obtained in the above-described manner can be planted and, after an initial growing period, subjected to a suitable selection by spraying. A further possibility consists in growing the seeds, if appropriate after sterilization, on agar plates using a suitable selection agent so that only the transformed seeds can grow into plants. Alternatively, the transformed plants are screened for the presence of a selectable marker such as the ones described above.

Following DNA transfer and regeneration, putatively transformed plants may also be evaluated, for instance using Southern analysis, for the presence of the gene of interest, copy number and/or genomic organisation. Alternatively or additionally, expression levels of the newly introduced DNA may be monitored using Northern and/or Western analysis, both techniques being well known to persons having ordinary skill in the art.

The generated transformed plants may be propagated by a variety of means, such as by clonal propagation or classical breeding techniques. For example, a first generation (or T1) transformed plant may be selfed and homozygous second-generation (or T2) transformants selected, and the T2 plants may then further be propagated through classical breeding techniques.

The generated transformed organisms may take a variety of forms. For example, they may be chimeras of transformed cells and non-transformed cells; clonal transformants (e.g., all cells transformed to contain the expression cassette); grafts of transformed and untransformed tissues (e.g., in plants, a transformed rootstock grafted to an untransformed scion).

The present invention clearly extends to any plant cell or plant produced by any of the methods described herein, and to all plant parts and propagules thereof. The present invention extends further to encompass the progeny of a primary transformed or transfected cell, tissue, organ or whole plant that has been produced by any of the aforementioned methods, the only requirement being that progeny exhibit the same genotypic and/or phenotypic characteristic(s) as those produced by the parent in the methods according to the invention.

The invention also includes host cells containing an isolated nucleic acid encoding a MADS15 protein as defined hereinabove. Preferred host cells according to the invention are plant cells.

Host plants for the nucleic acids or the vector used in the method according to the invention, the expression cassette or construct or vector are, in principle, advantageously all plants, which are capable of synthesizing the polypeptides used in the inventive method.

The invention also extends to harvestable parts of a plant such as, but not limited to seeds, leaves, fruits, flowers, stems, rhizomes, roots, tubers and bulbs. The invention furthermore relates to products derived, preferably directly derived, from a harvestable part of such a plant, such as dry pellets or powders, oil, fat and fatty acids, starch or proteins.

According to a preferred feature of the invention, the modulated expression is increased expression.

As mentioned above, a preferred method for modulating (preferably, increasing) expression of a nucleic acid encoding a MADS15 protein is by introducing and expressing in a plant a nucleic acid encoding a MADS15 protein; however the effects of performing the method, i.e. enhancing yield-related traits may also be achieved using other well known techniques. A description of some of these techniques will now follow.

One such technique is T-DNA activation tagging. The resulting transgenic plants show dominant phenotypes due to modified expression of genes close to the introduced promoter.

The effects of the invention may also be reproduced using the technique of TILLING (Targeted Induced Local Lesions In Genomes), or by homologous recombination.

Reference herein to enhanced yield-related traits is taken to mean an increase in biomass (weight) of one or more parts of a plant, which may include aboveground (harvestable) parts and/or (harvestable) parts below ground.

Taking corn as an example, a yield increase may be manifested as one or more of the following: increase in the number of plants established per hectare or acre, an increase in the number of ears per plant, an increase in the number of rows, number of kernels per row, kernel weight, thousand kernel weight, ear length/diameter, increase in the seed filling rate (which is the number of filled seeds divided by the total number of seeds and multiplied by 100), among others. Taking rice as an example, a yield increase may manifest itself as an increase in one or more of the following: number of plants per hectare or acre, number of panicles per plant, number of spikelets per panicle, number of flowers (florets) per panicle (which is expressed as a ratio of the number of filled seeds over the number of primary panicles), increase in the seed filling rate (which is the number of filled seeds divided by the total number of seeds and multiplied by 100), increase in thousand kernel weight, among others.

In a particular embodiment, such harvestable parts are roots, and performance of the methods of the invention results in plants having increased root growth relative to the root growth of suitable control plants. Root development is an essential determinant of plant growth and crop yield since the root is the main channel to extract nutrients from the environment.

Increased root yield may for example manifest itself as one of more of the following: a) increased amount of root biomass (whereby a discrimination between thick roots and thin roots may be made by defining a certain treshold), b) increased average root diameter, c) increased total root biomass, and d) increased root biomass/shoot biomass ratio. For the purpose of this invention, it should be understood that the term ‘root growth’ encompasses all aspects of growth of the different parts that make up the root system at different stages of its development, both in monocotyledonous and dicotyledonous plants. It is to be understood that enhanced growth of the root can result from enhanced growth of one or more of its parts including the primary root, lateral roots, adventitious roots, etc. all of which fall within the scope of this invention.

Since the transgenic plants according to the present invention have increased yield, it is likely that these plants exhibit an increased growth rate (during at least part of their life cycle), relative to the growth rate of control plants at a corresponding stage in their life cycle. The increased growth rate may be specific to one or more parts of a plant (including seeds), or may be throughout substantially the whole plant. Plants having an increased growth rate may have a shorter life cycle. The life cycle of a plant may be taken to mean the time needed to grow from a dry mature seed up to the stage where the plant has produced dry mature seeds, similar to the starting material. This life cycle may be influenced by factors such as early vigour, growth rate, greenness index, flowering time and speed of seed maturation. The increase in growth rate may take place at one or more stages in the life cycle of a plant or during substantially the whole plant life cycle. Increased growth rate during the early stages in the life cycle of a plant may reflect enhanced vigour. The increase in growth rate may alter the harvest cycle of a plant allowing plants to be sown later and/or harvested sooner than would otherwise be possible (a similar effect may be obtained with earlier flowering time). If the growth rate is sufficiently increased, it may allow for the further sowing of seeds of the same plant species (for example sowing and harvesting of rice plants followed by sowing and harvesting of further rice plants all within one conventional growing period). Similarly, if the growth rate is sufficiently increased, it may allow for the further sowing of seeds of different plants species (for example the sowing and harvesting of corn plants followed by, for example, the sowing and optional harvesting of soy bean, potato or any other suitable plant). Harvesting additional times from the same rootstock in the case of some crop plants may also be possible. Altering the harvest cycle of a plant may lead to an increase in annual biomass production per acre (due to an increase in the number of times (say in a year) that any particular plant may be grown and harvested). An increase in growth rate may also allow for the cultivation of transgenic plants in a wider geographical area than their wild-type counterparts, since the territorial limitations for growing a crop are often determined by adverse environmental conditions either at the time of planting (early season) or at the time of harvesting (late season). Such adverse conditions may be avoided if the harvest cycle is shortened. The growth rate may be determined by deriving various parameters from growth curves, such parameters may be: T-Mid (the time taken for plants to reach 50% of their maximal size) and T-90 (time taken for plants to reach 90% of their maximal size), amongst others.

According to a preferred feature of the present invention, performance of the methods of the invention gives plants having an increased growth rate relative to control plants. Therefore, according to the present invention, there is provided a method for increasing the growth rate of plants, which method comprises modulating expression, preferably increasing expression, in a plant of a nucleic acid encoding a MADS15 protein as defined herein.

An increase in yield and/or growth rate occurs whether the plant is under non-stress conditions or whether the plant is exposed to various stresses compared to control plants. Plants typically respond to exposure to stress by growing more slowly. In conditions of severe stress, the plant may even stop growing altogether. Mild stress on the other hand is defined herein as being any stress to which a plant is exposed which does not result in the plant ceasing to grow altogether without the capacity to resume growth. Mild stress in the sense of the invention leads to a reduction in the growth of the stressed plants of less than 40%, 35% or 30%, preferably less than 25%, 20% or 15%, more preferably less than 14%, 13%, 12%, 11% or 10% or less in comparison to the control plant under non-stress conditions. Due to advances in agricultural practices (irrigation, fertilization, pesticide treatments) severe stresses are not often encountered in cultivated crop plants. As a consequence, the compromised growth induced by mild stress is often an undesirable feature for agriculture. Mild stresses are the everyday biotic and/or abiotic (environmental) stresses to which a plant is exposed. Abiotic stresses may be due to drought or excess water, anaerobic stress, salt stress, chemical toxicity, oxidative stress and hot, cold or freezing temperatures. The abiotic stress may be an osmotic stress caused by a water stress (particularly due to drought), salt stress, oxidative stress or an ionic stress. Biotic stresses are typically those stresses caused by pathogens, such as bacteria, viruses, fungi and insects.

In particular, the methods of the present invention may be performed under non-stress conditions or under conditions of mild drought to give plants having increased yield relative to control plants. As reported in Wang et al. (Planta (2003) 218: 1-14), abiotic stress leads to a series of morphological, physiological, biochemical and molecular changes that adversely affect plant growth and productivity. Drought, salinity, extreme temperatures and oxidative stress are known to be interconnected and may induce growth and cellular damage through similar mechanisms. Rabbani et al. (Plant Physiol (2003) 133: 1755-1767) describes a particularly high degree of “cross talk” between drought stress and high-salinity stress. For example, drought and/or salinisation are manifested primarily as osmotic stress, resulting in the disruption of homeostasis and ion distribution in the cell. Oxidative stress, which frequently accompanies high or low temperature, salinity or drought stress, may cause denaturing of functional and structural proteins. As a consequence, these diverse environmental stresses often activate similar cell signaling pathways and cellular responses, such as the production of stress proteins, up-regulation of anti-oxidants, accumulation of compatible solutes and growth arrest. The term “non-stress” conditions as used herein are those environmental conditions that allow optimal growth of plants. Persons skilled in the art are aware of normal soil conditions and climatic conditions for a given location.

Performance of the methods of the invention gives plants grown under non-stress conditions or under mild drought conditions increased yield relative to control plants grown under comparable conditions. Therefore, according to the present invention, there is provided a method for increasing yield in plants grown under non-stress conditions or under mild drought conditions, which method comprises increasing expression in a plant of a nucleic acid encoding a MADS15 polypeptide.

Performance of the methods of the invention gives plants grown under conditions of nutrient deficiency, particularly under conditions of nitrogen deficiency, increased yield relative to control plants grown under comparable conditions. Therefore, according to the present invention, there is provided a method for increasing yield in plants grown under conditions of nutrient deficiency, which method comprises increasing expression in a plant of a nucleic acid encoding a MADS15 polypeptide. Nutrient deficiency may result from a lack or excess of nutrients such as nitrogen, phosphates and other phosphorous-containing compounds, potassium, calcium, cadmium, magnesium, manganese, iron and boron, amongst others.

In a preferred embodiment of the invention, the increase in yield and/or growth rate occurs according to the methods of the present invention under non-stress conditions.

The methods of the invention are advantageously applicable to any plant.

Plants that are particularly useful in the methods of the invention include all plants which belong to the superfamily Viridiplantae, in particular monocotyledonous and dicotyledonous plants including fodder or forage legumes, ornamental plants, food crops, trees or shrubs. According to a preferred embodiment of the present invention, the plant is a crop plant. Examples of crop plants include soybean, sunflower, canola, alfalfa, rapeseed, cotton, tomato, potato and tobacco. Further preferably, the plant is a monocotyledonous plant. Examples of monocotyledonous plants include sugarcane. More preferably the plant is a cereal. Examples of cereals include rice, maize, wheat, barley, millet, rye, triticale, sorghum and oats.

The present invention also encompasses use of nucleic acids encoding the MADS15 protein described herein and use of these MADS15 proteins in enhancing yield-related traits in plants.

Nucleic acids encoding the MADS15 protein described herein, or the MADS15 proteins themselves, may find use in breeding programmes in which a DNA marker is identified which may be genetically linked to a MADS15-encoding gene. The nucleic acids/genes, or the MADS15 proteins themselves may be used to define a molecular marker. This DNA or protein marker may then be used in breeding programmes to select plants having enhanced yield-related traits as defined hereinabove in the methods of the invention.

Allelic variants of a MADS15 protein-encoding nucleic acid/gene may also find use in marker-assisted breeding programmes. Such breeding programmes sometimes require introduction of allelic variation by mutagenic treatment of the plants, using for example EMS mutagenesis; alternatively, the programme may start with a collection of allelic variants of so called “natural” origin caused unintentionally. Identification of allelic variants then takes place, for example, by PCR. This is followed by a step for selection of superior allelic variants of the sequence in question and which give increased yield. Selection is typically carried out by monitoring growth performance of plants containing different allelic variants of the sequence in question. Growth performance may be monitored in a greenhouse or in the field. Further optional steps include crossing plants in which the superior allelic variant was identified with another plant. This could be used, for example, to make a combination of interesting phenotypic features.

Nucleic acids encoding MADS15 proteins may also be used as probes for genetically and physically mapping the genes that they are a part of, and as markers for traits linked to those genes. Such information may be useful in plant breeding in order to develop lines with desired phenotypes. Such use of MADS15 protein-encoding nucleic acids requires only a nucleic acid sequence of at least 15 nucleotides in length. The MADS15 protein-encoding nucleic acids may be used as restriction fragment length polymorphism (RFLP) markers. Southern blots (Sambrook J, Fritsch E F and Maniatis T (1989) Molecular Cloning, A Laboratory Manual) of restriction-digested plant genomic DNA may be probed with the MADS15 protein-encoding nucleic acids. The resulting banding patterns may then be subjected to genetic analyses using computer programs such as MapMaker (Lander et al. (1987) Genomics 1: 174-181) in order to construct a genetic map. In addition, the nucleic acids may be used to probe Southern blots containing restriction endonuclease-treated genomic DNAs of a set of individuals representing parent and progeny of a defined genetic cross. Segregation of the DNA polymorphisms is noted and used to calculate the position of the MADS15 protein-encoding nucleic acid in the genetic map previously obtained using this population (Botstein et al. (1980) Am. J. Hum. Genet. 32:314-331).

The production and use of plant gene-derived probes for use in genetic mapping is described in Bernatzky and Tanksley (1986) Plant Mol. Biol. Reporter 4: 37-41. Numerous publications describe genetic mapping of specific cDNA clones using the methodology outlined above or variations thereof. For example, F2 intercross populations, backcross populations, randomly mated populations, near isogenic lines, and other sets of individuals may be used for mapping. Such methodologies are well known to those skilled in the art.

The nucleic acid probes may also be used for physical mapping (i.e., placement of sequences on physical maps; see Hoheisel et al. In: Non-mammalian Genomic Analysis: A Practical Guide, Academic press 1996, pp. 319-346, and references cited therein).

In another embodiment, the nucleic acid probes may be used in direct fluorescence in situ hybridisation (FISH) mapping (Trask (1991) Trends Genet. 7:149-154). Although current methods of FISH mapping favour use of large clones (several kb to several hundred kb; see Laan et al. (1995) Genome Res. 5:13-20), improvements in sensitivity may allow performance of FISH mapping using shorter probes.

A variety of nucleic acid amplification-based methods for genetic and physical mapping may be carried out using the nucleic acids. Examples include allele-specific amplification (Kazazian (1989) J. Lab. Clin. Med. 11:95-96), polymorphism of PCR-amplified fragments (CAPS; Sheffield et al. (1993) Genomics 16:325-332), allele-specific ligation (Landegren et al. (1988) Science 241:1077-1080), nucleotide extension reactions (Sokolov (1990) Nucleic Acid Res. 18:3671), Radiation Hybrid Mapping (Walter et al. (1997) Nat. Genet. 7:22-28) and Happy Mapping (Dear and Cook (1989) Nucleic Acid Res. 17:6795-6807). For these methods, the sequence of a nucleic acid is used to design and produce primer pairs for use in the amplification reaction or in primer extension reactions. The design of such primers is well known to those skilled in the art. In methods employing PCR-based genetic mapping, it may be necessary to identify DNA sequence differences between the parents of the mapping cross in the region corresponding to the instant nucleic acid sequence. This, however, is generally not necessary for mapping methods.

The methods according to the present invention result in plants having enhanced yield-related traits, as described hereinbefore. These traits may also be combined with other economically advantageous traits, such as further yield-enhancing traits, tolerance to other abiotic and biotic stresses, traits modifying various architectural features and/or biochemical and/or physiological features.

Detailed Description of MADS15 Down

It has now surprisingly been found that decreasing the level and/or activity of an endogenous MADS15 polypeptide gives plants having enhanced yield-related traits, in particular increased yield relative, to corresponding wild type plants. The present invention therefore provides methods for enhancing yield related traits, particularly for increasing yield of a plant relative to control plants, comprising decreasing the level and/or activity of an endogenous MADS15 polypeptide. Reference herein to “control plants” is taken to mean corresponding wild type plants in which there is no reduction in activity of the endogenous MADS15 polypeptide.

Advantageously, performance of the methods according to the present invention results in plants having increased yield, particularly increased seed yield and/or increased biomass, relative to corresponding wild type plants.

The term “increased yield” as defined herein is taken to mean an increase in biomass (weight) of one or more parts of a plant, which may include aboveground (harvestable) parts and/or (harvestable) parts below ground.

In particular, such harvestable parts include vegetative biomass and/or seeds, and performance of the methods of the invention results in plants having increased yield (in vegetative biomass and/or seed) relative to the yield of control plants.

Taking corn as an example, a yield increase may be manifested as one or more of the following: increase in the number of plants per hectare or acre, an increase in the number of ears per plant, an increase in the number of rows, number of kernels per row, kernel weight, thousand kernel weight, ear length/diameter, increase in the seed filling rate (which is the number of filled seeds divided by the total number of seeds and multiplied by 100), among others. Taking rice as an example, a yield increase may manifest itself as an increase in one or more of the following: number of plants per hectare or acre, number of panicles per plant, number of spikelets per panicle, number of flowers (florets) per panicle (which is expressed as a ratio of the number of filled seeds over the number of primary panicles), increase in the seed filling rate (which is the number of filled seeds divided by the total number of seeds and multiplied by 100), increase in thousand kernel weight, among others.

The increase in seed yield may also be manifested as an increase in seed size and/or seed volume. This may increase the amount, or change the composition of, substances in the seed, such as oils, proteins and carbohydrates.

According to a preferred feature, performance of the methods of the invention result in plants having increased yield, particularly increased biomass and/or seed yield. Therefore, according to the present invention, there is provided a method for increasing plant yield, which method comprises decreasing the level of activity of a MADS15 polypeptide or a homologue thereof, preferably by downregulating expression of a MADS15 gene or a homologue thereof.

Since the transgenic plants according to the present invention have increased yield, it is likely that these plants exhibit an increased growth rate (during at least part of their life cycle), relative to the growth rate of corresponding wild type plants at a corresponding stage in their life cycle. The increased growth rate may be specific to one or more parts of a plant (including seeds), or may be throughout substantially the whole plant. Plants having an increased growth rate may have a shorter life cycle. The life cycle of a plant may be taken to mean the time needed to grow from a dry mature seed up to the stage where the plant has produced dry mature seeds, similar to the starting material. This life cycle may be influenced by factors such as early vigour, growth rate, flowering time and speed of seed maturation. An increase in growth rate may take place at one or more stages in the life cycle of a plant or during substantially the whole plant life cycle. Increased growth rate during the early stages in the life cycle of a plant may reflect enhanced vigour. The increase in growth rate may alter the harvest cycle of a plant allowing plants to be sown later and/or harvested sooner than would otherwise be possible (a similar effect may be obtained with earlier flowering time). If the growth rate is sufficiently increased, it may allow for the further sowing of seeds of the same plant species (for example sowing and harvesting of rice plants followed by sowing and harvesting of further rice plants all within one conventional growing period). Similarly, if the growth rate is sufficiently increased, it may allow for the further sowing of seeds of different plants species (for example the sowing and harvesting of corn plants followed by, for example, the sowing and optional harvesting of soy bean, potato or any other suitable plant). Harvesting additional times from the same rootstock in the case of some crop plants may also be possible. Altering the harvest cycle of a plant may lead to an increase in annual biomass production per acre (due to an increase in the number of times (say in a year) that any particular plant may be grown and harvested). An increase in growth rate may also allow for the cultivation of transgenic plants in a wider geographical area than their wild-type counterparts, since the territorial limitations for growing a crop are often determined by adverse environmental conditions either at the time of planting (early season) or at the time of harvesting (late season). Such adverse conditions may be avoided if the harvest cycle is shortened. The growth rate may be determined by deriving various parameters from growth curves, such parameters may be: T-Mid (the time taken for plants to reach 50% of their maximal size) and T-90 (time taken for plants to reach 90% of their maximal size), amongst others.

Performance of the methods of the invention gives plants having an increased growth rate. Therefore, according to the present invention, there is provided a method for increasing the growth rate of plants relative to control plants, which method comprises preferentially reducing the expression level and/or activity of an endogenous MADS15 gene in a plant.

An increase in yield and/or growth rate occurs whether the plant is under non-stress conditions or whether the plant is exposed to various stresses compared to control plants. Plants typically respond to exposure to stress by growing more slowly. In conditions of severe stress, the plant may even stop growing altogether. Mild stress on the other hand is defined herein as being any stress to which a plant is exposed which does not result in the plant ceasing to grow altogether without the capacity to resume growth. Mild stress in the sense of the invention leads to a reduction in the growth of the stressed plants of less than 40%, 35% or 30%, preferably less than 25%, 20% or 15%, more preferably less than 14%, 13%, 12%, 11% or 10% or less in comparison to the control plant under non-stress conditions. Due to advances in agricultural practices (irrigation, fertilization, pesticide treatments) severe stresses are not often encountered in cultivated crop plants. As a consequence, the compromised growth induced by mild stress is often an undesirable feature for agriculture. Mild stresses are the everyday biotic and/or abiotic (environmental) stresses to which a plant is exposed. Abiotic stresses may be due to drought or excess water, anaerobic stress, salt stress, chemical toxicity, oxidative stress and hot, cold or freezing temperatures. The abiotic stress may be an osmotic stress caused by a water stress (particularly due to drought), salt stress, oxidative stress or an ionic stress. Biotic stresses are typically those stresses caused by pathogens, such as bacteria, viruses, fungi and insects.

In particular, the methods of the present invention may be performed under non-stress conditions or under conditions of mild drought to give plants having increased yield relative to control plants. As reported in Wang et al. (Planta (2003) 218: 1-14), abiotic stress leads to a series of morphological, physiological, biochemical and molecular changes that adversely affect plant growth and productivity. Drought, salinity, extreme temperatures and oxidative stress are known to be interconnected and may induce growth and cellular damage through similar mechanisms. Rabbani et al. (Plant Physiol (2003) 133: 1755-1767) describes a particularly high degree of “cross talk” between drought stress and high-salinity stress. For example, drought and/or salinisation are manifested primarily as osmotic stress, resulting in the disruption of homeostasis and ion distribution in the cell. Oxidative stress, which frequently accompanies high or low temperature, salinity or drought stress, may cause denaturing of functional and structural proteins. As a consequence, these diverse environmental stresses often activate similar cell signaling pathways and cellular responses, such as the production of stress proteins, up-regulation of anti-oxidants, accumulation of compatible solutes and growth arrest. The term “non-stress” conditions as used herein are those environmental conditions that allow optimal growth of plants. Persons skilled in the art are aware of normal soil conditions and climatic conditions for a given location.

Performance of the methods of the invention gives plants grown under non-stress conditions or under mild drought conditions increased yield relative to control plants grown under comparable conditions. Therefore, according to the present invention, there is provided a method for increasing yield in plants grown under non-stress conditions or under mild drought conditions, which method comprises reducing expression of an endogenous MADS15 gene in a plant.

Performance of the methods of the invention gives plants grown under conditions of nutrient deficiency, particularly under conditions of nitrogen deficiency, increased yield relative to control plants grown under comparable conditions. Therefore, according to the present invention, there is provided a method for increasing yield in plants grown under conditions of nutrient deficiency, which method comprises decreasing expression in a plant of a nucleic acid encoding a MADS15 polypeptide. Nutrient deficiency may result from a lack or excess of nutrients such as nitrogen, phosphates and other phosphorous-containing compounds, potassium, calcium, cadmium, magnesium, manganese, iron and boron, amongst others.

In a preferred embodiment of the invention, the increase in yield and/or growth rate occurs according to the methods of the present invention under non-stress conditions.

The methods of the invention are advantageously applicable to any plant. Plants that are particularly useful in the methods of the invention include all plants which belong to the superfamily Viridiplantae, in particular monocotyledonous and dicotyledonous plants including fodder or forage legumes, ornamental plants, food crops, trees or shrubs. According to a preferred embodiment of the present invention, the plant is a crop plant.

Examples of crop plants include soybean, sunflower, canola, alfalfa, rapeseed, cotton, tomato, potato and tobacco. Further preferably, the plant is a monocotyledonous plant. Examples of monocotyledonous plants include sugarcane. More preferably the plant is a cereal. Examples of cereals include rice, maize, wheat, barley, millet, rye, triticale, sorghum and oats.

Reference herein to a “decrease” in level of an endogenous MADS15 protein in a plant is taken to mean a reduction in protein concentration or substantial elimination of an endogenous MADS15 protein relative to endogenous MADS15 protein levels found in corresponding wild type plants. This reduction or substantial elimination may result in reduced or substantially abolished MADS15 protein activity in a plant.

Reference herein to a “decrease” in activity of an endogenous MADS15 protein in a plant is taken to mean a reduction in MADS15 protein activity or substantial elimination of activity of an endogenous MADS15 protein relative to endogenous MADS15 protein activity levels found wild type plants.

Preferably, the reduction in endogenous MADS15 protein level and/or activity is obtained by downregulating the expression of the endogenous MADS15 gene.

Reference herein to an “endogenous” MADS15 gene not only refers to MADS15 genes as found in a plant in its natural form (i.e., without there being any human intervention), but also refers to isolated MADS15 genes subsequently introduced into a plant. For example, a transgenic plant containing a MADS15 transgene may encounter a reduction or substantial elimination of the MADS15 transgene expression and/or reduced or substantial elimination of expression of an endogenous MADS15 gene.

This reduction (or substantial elimination) of endogenous MADS15 gene expression may be achieved using any one or more of several well-known gene silencing methods. “Gene silencing” or “downregulation” of expression, as used herein, refers to a reduction or the substantial elimination of MADS15 gene expression and/or MADS15 polypeptide levels and/or MADS15 polypeptide activity.

One such method for reduction or substantial elimination of endogenous MADS15 gene expression is RNA-mediated downregulation of gene expression (RNA silencing). Silencing in this case is triggered in a plant by a double stranded RNA molecule (dsRNA) that is substantially homologous to a target MADS15 gene. This dsRNA is further processed by the plant into about 21 to about 26 nucleotides called short interfering RNAs (siRNAs). The siRNAs are incorporated into an RNA-induced silencing complex (RISC) that cleaves the mRNA of a MADS15 target gene, thereby reducing or substantially eliminating the number of MADS15 mRNAs to be translated into a MADS15 protein.

One example of an RNA silencing method involves the introduction of coding sequences or parts thereof in a sense orientation into a plant. The additional gene, or part thereof, will silence an endogenous MADS15 gene, giving rise to a phenomenon known as co-suppression. The reduction of MADS15 gene expression will be more pronounced if several additional copies are introduced into the plant, as there is a positive correlation between high transcript levels and the triggering of co-suppression.

Another example of an RNA silencing method involves the use of antisense MADS15 nucleic acid sequences.

The antisense nucleic acid can be produced biologically using an expression vector into which a nucleic acid has been subcloned in an antisense orientation (i.e., RNA transcribed from the inserted nucleic acid will be of an antisense orientation to a target nucleic acid of interest, described further in the following subsection). Preferably, production of antisense nucleic acids in plants occurs by means of a stably integrated transgene comprising a promoter operative for constitutive expression in plants, an antisense oligonucleotide, and a terminator.

A preferred method for reduction or substantial elimination of endogenous MADS15 gene expression via RNA silencing is by using an expression vector into which a MADS15 gene or fragment thereof has been cloned as an inverted repeat (in part or completely), separated by a spacer (non-coding DNA).

In still another embodiment, the reduction or substantial elimination of endogenous MADS15 exprssion may be obtained by using ribozymes. For example, a derivative of a Tetrahymena L-19 IVS RNA can be constructed in which the nucleotide sequence of the active site is complementary to the nucleotide sequence to be cleaved in an MADS15-encoding mRNA.

Gene silencing may also be achieved by insertion mutagenesis or if there is a mutation on the endogenous MADS15 gene and/or a mutation on an isolated MADS15 gene subsequently introduced into a plant. The reduction or substantial elimination of MADS15 protein activity may be caused by a non-functional MADS15. For example, MADS15 binds to various interacting proteins; one or more mutation(s) and/or truncation(s) within the MADS box of a MADS15 may therefore provide for a MADS15 protein that is still able to bind interacting proteins but that cannot exhibit its normal function as transcription factor.

A further approach to gene silencing is by targeting nucleotide sequences complementary to the regulatory region of the MADS15 gene (e.g., the MADS15 promoter and/or enhancers) to form triple helical structures that prevent transcription of the MADS15 gene in target cells.

Still another approach to gene silencing is described by Hiratsu et al. (Plant J. 34, 733-739, 2003). This method does not depend on sequence homology to the targeted gene but involves the use of a repression sequence domain in transcriptional gene fusions, and has been used to modify traits of agronomic interest (Fujita et al., Plant Cell 17, 3470-3488, 2005 and Mitsuda at al., Plant Cell 17, 2993-3006, 2005). Typically, a nucleotide chimeric fusion is made between a gene encoding a protein capable of positively influencing the expression of the targeted gene (such as a transcription activator), and a nucleotide fragment encoding a repression domain. Upon expression of the chimeric gene fusion, the expression of the targeted gene is repressed, usually in a dominant negative fashion. Repression domains are well known in the art, for example the EAR motif present in some AP2 and Zinc finger transcription factor. Methods based on repression domains are well suited to overcome gene redundancy for the targeted gene in the plant species of choice.

Described above are examples of various methods for gene silencing (for the reduction or substantial elimination of endogenous MADS15 gene expression. The methods of the invention rely on the reduction of expression of an endogenous MADS15 gene in a plant. A person skilled in the art would readily be able to adapt the aforementioned methods for silencing so as to achieve gene silencing in a whole plant or in parts thereof through the use of an appropriate promoter, for example.

It should be noted that the essence of the present invention resides in the advantageous and surprising results found upon reduction or substantial elimination of endogenous MADS15 gene expression in a plant, and is not limited to any particular method for such reduction or substantial elimination of endogenous MADS15 protein activity. The activity of a MADS15 polypeptide may also be decreased or eliminated by introducing a genetic modification (preferably in the locus of a MADS15 gene). The locus of a gene as defined herein is taken to mean a genomic region, which includes the gene of interest and 10 kb up- or down stream of the coding region.

The genetic modification may be introduced, for example, by any one (or more) of the following methods: T-DNA inactivation, TILLING, site-directed mutagenesis, directed evolution, homologous recombination. Following introduction of the genetic modification, there follows a step of selecting for decreased activity of a MADS15 polypeptide, which decrease in activity gives plants having increased yield.

T-DNA inactivation tagging involves insertion of a T-DNA, in the genomic region of the gene of interest or 10 kb up- or downstream of the coding region of a gene in a configuration such that the T-DNA inhibits expression of the targeted gene. Typically, regulation of expression of the targeted gene by its natural promoter is disrupted. The T-DNA is randomly inserted into the plant genome, for example, through Agrobacterium infection and leads to down-regulated expression of genes near the inserted T-DNA. The resulting transgenic plants show phenotypes due to inhibited expression of genes close to the introduced T-DNA.

A genetic modification may also be introduced in the locus of a MADS15 gene using the technique of TILLING (Targeted Induced Local Lesions In Genomes).

Site-directed mutagenesis and random mutagenesis may be used to generate variants of MADS15 nucleic acids. Several methods are available to achieve site-directed mutagenesis, the most common being PCR based methods (current protocols in molecular biology. Wiley Eds.).

Directed evolution may also be used to generate variants of MADS15 nucleic acids. This consists of iterations of DNA shuffling followed by appropriate screening and/or selection to generate variants of MADS15 nucleic acids or variants thereof encoding MADS15 polypeptides having a modified (here decreased or abolished) biological activity (Castle et al., (2004) Science 304(5674): 1151-4; U.S. Pat. Nos. 5,811,238 and 6,395,547).

T-DNA activation, TILLING, site-directed mutagenesis and directed evolution are examples of technologies that enable the generation of novel alleles and MADS15 variants.

The effects of the invention may also be reproduced using homologous recombination. The nucleic acid to be targeted may be an allele encoding an inactive protein or a protein with decreased activity, used to replace the endogenous gene or may be introduced in addition to the endogenous gene, and needs to be targeted to the locus of the MADS15 gene.

Other methods, such as the use of antibodies directed to the endogenous MADS15 for inhibiting its function in planta, or interference in the signalling pathway in which MADS15 is involved, will be well known to the skilled man. Alternatively, a screening program may be set up to identify natural variants of a MADS15 gene, which variants have reduced MADS15 activity, or no MADS15 activity at all. Such natural variants may also be used in the methods of the present invention.

For optimal performance, the gene silencing techniques used for the reduction or substantial elimination of endogenous MADS15 gene expression requires the use of MADS15 nucleic acid sequences from monocotyledonous plants for transformation into monocotyledonous plants. Preferably, a MADS15 nucleic acid from any given plant species is introduced into that same species. For example, a MADS15 nucleic acid from rice (be it a full length MADS15 sequence or a fragment) is transformed into a rice plant. The MADS15 nucleic acid need not be introduced into the same plant variety.

Reference herein to a “MADS15 gene” or a “MADS15 nucleic acid” is taken to mean a polymeric form of a deoxyribonucleotide or a ribonucleotide polymer of any length, either double- or single-stranded, or analogues thereof, that have the essential characteristic of a natural ribonucleotide in that they can hybridise to nucleic acids in a manner similar to naturally occurring polynucleotides. A “MADS15 gene” or a “MADS15 nucleic acid” refers to a sufficient length of substantially contiguous nucleotides of a MADS15-encoding gene to perform gene silencing; this may be as little as 20 or fewer nucleotides. A gene encoding a (functional) protein is not a requirement for the various methods discussed above for the reduction or substantial elimination of expression of an endogenous MADS15 gene.

The methods of the invention may be performed using a sufficient length of substantially contiguous nucleotides of a MADS15 gene/nucleic acid, which may consist of 20 or fewer nucleotides, which may be from any part of the MADS15 gene/nucleic acid, such as the 5′ end of the coding region that is well conserved amongst the MADS15 gene family, or encoding one of the conserved motifs described below.

MADS15 genes are well known in the art and useful in the methods of the invention are substantially contiguous nucleotides of the plant MADS15 genes/nucleic acid described in Moon et al. (Plant Physiol. 120, 1193-1204, 1999).

Other MADS15 gene/nucleic acid sequences may also be used in the methods of the invention, and may readily be identified by a person skilled in the art. MADS15 polypeptides may be identified by the presence of one or more of several well-known features (see below). Upon identification of a MADS15 polypeptide, a person skilled in the art could easily derive, using routine techniques, the corresponding encoding nucleic acid sequence and use a sufficient length of contiguous nucleotides of the same to perform any one or more of the gene silencing methods described above.

The term “MADS15 polypeptide or homologue thereof” as defined herein refers to a protein that falls in the group of FUL-like MADS box proteins as delineated by Adam et al. (J. Mol. Evol. 62, 15-31). FUL-like MADS box proteins are part of the SQUAMOSA subfamily and have the typical MIKC^(c) architecture: a MADS domain (M) at the N-terminus, followed by an intervening domain (I) involved in dimerisation, a highly conserved keratin domain (K) and a variable domain (C) at the C-terminus, which is responsible for binding of interacting proteins or transcriptional activation (De Bodt et al. Trends in Plant Science 8, 475-483).

Plant MADS15 polypeptides may also be identified by the presence of certain conserved motifs. The presence of these conserved motifs may be identified using methods for the alignment of sequences for comparison as described hereinabove. In some instances, the default parameters may be adjusted to modify the stringency of the search. For example using BLAST, the statistical significance threshold (called “expect” value) for reporting matches against database sequences may be increased to show less stringent matches. This way, short nearly exact matches may be identified. Upon identification of a MADS15 polypeptide by the presence of these motifs, a person skilled in the art may easily derive the corresponding nucleic acid encoding the polypeptide comprising the relevant motifs, and use a sufficient length of contiguous nucleotides of the same to perform any one or more of the gene silencing methods described above (for the reduction or substantial elimination of an endogenous MADS15 gene expression).

Typically, the presence of at least one of the motifs 1 to 4 should be sufficient to identify any query sequence as a MADS15, however the presence of at least motifs 1 and 2 is preferred. The consensus sequence provided is based on the monocot sequences given in the sequence listing. A person skilled in the art would be well aware that the consensus sequence may vary somewhat if further or different sequences (for example from dicot sequences) were used for comparison.

Motif 1, located in the MADS domain (SEQ ID NO: 114):

L(L/V)KKA(H/N)EIS(VI)L(C/Y)DAE(V/I/L) (A/G) (L/A/V) (I/V) (I/V)FS(T/P/A/N)KGKLYE(Y/F) (A/S) (T/S) (D/N/E)S(K/C/R/S)M(D/E) (N/I/R/K)IL(E/D)R.

Preferably, this conserved sequence motif 1 has the sequence:

LLKKAHEISVLCDAEVA(L/A/V)I(I/V)FS(T/P)KGKLYEYATDS (C/R)M(D/E) (R/K)ILER, most preferably the conserved sequence motif 1 has the sequence:

LLKKAHEISVLCDAEVAAIVFSPKGKLYEYATDSRMDKILER

Motif 2, located in the K domain (SEQ ID NO: 115):

KLK(A/S) (K/R) (V/I)E(A/T/S) (L/I) (Q/N) (K/R/N) (S/C/R) (Q/H) (R/K)HLMGE

Preferably, this conserved sequence motif 2 has the sequence:

KLKAK(V/I)E(A/T) (L/I)QK(S/C) (Q/H) (R/K)HLMGE

More preferably, this conserved sequence motif 2 has the sequence:

KLKAKIETIQKCHKHLMGE

Optionally, the MADS15 polypeptide or its homologue may comprise in the C domain motif 3 and/or motif 4:

motif 3 (SEQ ID NO: 116): Q(P/Q/V/A)QTS(S/F) (S/F) (S/F) (S/F) (S/C/F) (F/M) motif 4 (SEQ ID NO: 117): (G/A/V/L) (L/P)XWMX(S/H) wherein the first X residue in motif 4 may be any amino acid, but preferably L, P or H; and wherein the second X residue may be any amino acid, but preferably V or L.

Alternatively, the C-domain (starting behind the keratin domain, i.e. at R175 in SEQ ID NO: 110) may be characterised by the increased occurrence of glutamine (normally 3.93%, here at least 8.77% with a maximum of 26.73%), in addition, the content in alanine, proline, and/or serine may also be increased (above 7.8%, 4.85% and 6.89% respectively).

Alternatively formulated, a preferred MADS15 protein useful in the methods of the present invention comprises at least an N-terminal MADS domain corresponding to the SMART domain SM00432 (Pfam PF00319) followed by a Keratin domain corresponding to the K-box region defined in Pfam as PF01486, more preferably, the MADS15 protein has in its MADS domain the conserved signature of SEQ ID NO: 114 and in its K-domain the conserved signature of SEQ ID NO: 115, most preferably, the MADS15 protein has the sequence given in SEQ ID NO: 110.

Homologues, as defined above, may readily be identified using routine techniques well known in the art, such as by sequence alignment; homologues of OsMADS15 may have been named differently in various plant species, therefore the gene/protein names should not be used for identifying orthologues or paralogues. Methods for the alignment of sequences for comparison are well known in the art, such methods include GAP, BESTFIT, BLAST, FASTA and TFASTA. GAP uses the algorithm of Needleman and Wunsch ((1970) J Mol Biol 48: 443-453) to find the alignment of two complete sequences that maximizes the number of matches and minimizes the number of gaps. The BLAST algorithm (Altschul et al. (1990) J Mol Biol 215: 403-10) calculates percent sequence identity and performs a statistical analysis of the similarity between the two sequences. The software for performing BLAST analysis is publicly available through the National Centre for Biotechnology Information. Homologous sequences may readily be identified using, for example, the ClustalW multiple sequence alignment algorithm (version 1.83), with the default pairwise alignment parameters, and a scoring method in percentage. Minor manual editing may be performed to optimise alignment between conserved motifs (see below), as would be apparent to a person skilled in the art.

The various structural domains in a MADS15 protein may be identified using specialised databases e.g. SMART (Schultz et al. (1998) Proc. Natl. Acad. Sci. USA 95, 5857-5864; Letunic et al. (2002) Nucleic Acids Res 30, 242-244), InterPro (Mulder et al., (2003) Nucl. Acids. Res. 31, 315-318;), Prosite (Bucher and Bairoch (1994), A generalized profile syntax for biomolecular sequences motifs and its function in automatic sequence interpretation. (In) ISMB-94; Proceedings 2nd International Conference on Intelligent Systems for Molecular Biology. Altman R., Brutlag D., Karp P., Lathrop R., Searls D., Eds., pp 53-61, AAAIPress, Menlo Park; Hulo et al., Nucl. Acids. Res. 32:D134-D137, (2004)) or Pfam (Bateman et al., Nucleic Acids Research 30(1): 276-280 (2002)).

Furthermore, a MADS15 protein may also be identifiable by its ability to bind DNA and to interact with other proteins. DNA-binding activity and protein-protein interactions may readily be determined in vitro or in vivo using techniques well known in the art. Examples of in vitro assays for DNA binding activity include: gel retardation analysis using known MADS-box DNA binding domains (West et al. (1998) Nucl Acid Res 26(23): 5277-87), or yeast one-hybrid assays. An example of an in vitro assay for protein-protein interactions is the yeast two-hybrid analysis (Fields and Song (1989) Nature 340:245-6). Proteins known to interact with OsMADS15 include other MADS proteins (such as those involved in the flowering signalling complex), receptor like kinases such a Clavata1 and Clavata2, Erecta, BR11 or RSK.

Therefore upon identification of a MADS15 polypeptide using one or several of the features described above, a person skilled in the art may easily derive the corresponding nucleic acid encoding the polypeptide, and use a sufficient length of substantially contiguous nucleotides of the same to perform any one or more of the gene silencing methods described above (for the reduction or substantial elimination of an endogenous MADS15 gene expression).

Preferred for use in the methods of the invention is a sufficient length of substantially contiguous nucleotides of SEQ ID NO: 109 (OsMADS15), or the use of a sufficient length of substantially contiguous nucleotides of a nucleic acid sequence encoding an orthologue or paralogue of OsMADS15 (SEQ ID NO: 109). Examples of such orthologues and paralogues of OsMADS15 are provided in Table D below. Close homologues of OsMADS15 are the proteins represented by SEQ ID NO: 147, 149, 151, 153, 155, 157, 159, 161, 163, 165, 167, 169, 171 and 173.

Orthologues in, for example, monocot plant species may easily be found by performing a so-called reciprocal blast search. This may be done by a first blast involving blasting a query sequence (for example, SEQ ID NO: 109 or SEQ ID NO: 110) against any sequence database, such as the publicly available NCBI database. BLASTN or TBLASTX (using standard default values) may be used when starting from a nucleotide sequence and BLASTP or TBLASTN (using standard default values) may be used when starting from a protein sequence. The BLAST results may optionally be filtered. The full-length sequences of either the filtered results or non-filtered results are then BLASTed back (second BLAST) against sequences from the organism from which the query sequence is derived (where the query sequence is SEQ ID NO: 109 or SEQ ID NO: 110 the second blast would therefore be against rice sequences). The results of the first and second BLASTs are then compared. A paralogue is identified if a high-ranking hit from the first blast is from the same species as from which the query sequence is derived; an orthologue is identified if a high-ranking hit is not from the same species as from which the query sequence is derived. High-ranking hits are those having a low E-value. The lower the E-value, the more significant the score (or in other words the lower the chance that the hit was found by chance). Computation of the E-value is well known in the art. In the case of large families, ClustalW may be used, followed by a neighbour joining tree, to help visualize clustering of related genes and to identify orthologues and paralogues.

The source of the substantially contiguous nucleotides of a MADS15 gene/nucleic acid may be any plant source or artificial source. For optimal performance, the gene silencing techniques used for the reduction or substantial elimination of endogenous MADS15 gene expression requires the use of MADS15 sequences from monocotyledonous plants for transformation into monocotyledonous plants. Preferably, MADS15 sequences from the family Poaceae are transformed into plants of the family Poaceae. Further preferably, a MADS15 nucleic acid from rice (be it a full length MADS15 sequence or a fragment) is transformed into a rice plant. The MADS15 nucleic acid need not be introduced into the same plant variety. Most preferably, the MADS15 nucleic acid from rice is a sufficient length of substantially contiguous nucleotides of SEQ ID NO: 109 (OsMADS15) or a sufficient length of substantially contiguous nucleotides of a nucleic acid sequence encoding an orthologue or paralogue of OsMADS15 (SEQ ID NO: 110). As mentioned above, a person skilled in the art would be well aware of what would constitute a sufficient length of substantially contiguous nucleotides to perform any of the gene silencing methods defined hereinabove, this may be as little as 20 or fewer substantially contiguous nucleotides in some cases.

The invention also provides genetic constructs and vectors to facilitate introduction and/or expression of the nucleotide sequences useful in the methods according to the invention.

Therefore, there is provided a gene construct comprising one or more control sequences capable of driving expression of a sense and/or antisense MADS15 nucleic acid sequence in a plant so as to silence an endogenous MADS15 gene in the plant; and optionally a transcription termination sequence. Preferably, the control sequence is a constitutive and ubiquitous promoter.

A preferred construct for gene silencing is one comprising an inverted repeat of a MADS15 gene or fragment thereof, preferably capable of forming a hairpin structure, which inverted repeat is under the control of a constitutive promoter.

Therefore, the invention provides a construct comprising:

-   -   (a) a MADS15 nucleic acid capable of forming a hairpin         structure;     -   (b) one or more control sequences capable of driving expression         of the nucleic acid sequence of (a); and optionally     -   (c) a transcription termination sequence.

Constructs useful in the methods according to the present invention may be created using recombinant DNA technology well known to persons skilled in the art. The gene constructs may be inserted into vectors, which may be commercially available, suitable for transforming into plants and suitable for expression of the gene of interest in the transformed cells. The invention therefore provides use of a gene construct as defined hereinabove in the methods of the invention.

The sequence of interest is operably linked to one or more control sequences (at least to a promoter) capable of increasing expression in a plant.

Advantageously, any type of promoter may be used to drive expression of the nucleic acid sequence. The promoter may be an inducible promoter, i.e. having induced or increased transcription initiation in response to a developmental, chemical, environmental or physical stimulus. Additionally or alternatively, the promoter may be a tissue-preferred or cell-preferred promoter, i.e. one that is capable of preferentially initiating transcription in certain tissues, such as the leaves, roots, seed tissue etc, or even in specific cells. Promoters able to initiate transcription in certain tissues or cells only are referred to herein as “tissue-specific”, respectively “cell-specific”.

Preferably, the MADS15 nucleic acid or functional variant thereof is operably linked to a constitutive promoter. Preferably the promoter is a ubiquitous promoter and is expressed predominantly throughout the plant. Preferably, the constitutive promoter capable of preferentially expressing the nucleic acid throughout the plant has a comparable expression profile to a GOS2 promoter. More preferably, the constitutive promoter has the same expression profile as the rice GOS2 promoter, most preferably, the promoter capable of preferentially expressing the nucleic acid throughout the plant is the GOS2 promoter from rice (SEQ ID NO: 113 or SEQ ID NO: 174). It should be clear that the applicability of the present invention is not restricted to the MADS15 nucleic acid represented by SEQ ID NO: 109, nor is the applicability of the invention restricted to expression of a MADS15 nucleic acid when driven by a GOS2 promoter. An alternative constitutive promoter that is useful in the methods of the present invention is the high mobility group protein promoter (PRO0170, SEQ ID NO: 40 in WO2004070039). Examples of other constitutive promoters that may also be used to drive expression of a MADS15 nucleic acid are shown in the definitions section.

Optionally, one or more terminator sequences may also be used in the construct introduced into a plant. Additional regulatory elements may include transcriptional as well as translational enhancers. Those skilled in the art will be aware of terminator and enhancer sequences that may be suitable for use in performing the invention. Such sequences would be known or may readily be obtained by a person skilled in the art.

The genetic constructs of the invention may further include an origin of replication sequence that is required for maintenance and/or replication in a specific cell type. One example is when a genetic construct is required to be maintained in a bacterial cell as an episomal genetic element (e.g. plasmid or cosmid molecule). Preferred origins of replication include, but are not limited to, the f1-ori and colE1. The genetic construct may optionally comprise a selectable marker gene.

The present invention also encompasses plants including plant parts obtainable by the methods according to the present invention having increased yield relative to control plants and which have reduced or substantially eliminated expression of an endogenous MADS15 gene.

The invention furthermore provides a method for the production of transgenic plants having increased yield relative to control plants, which transgenic plants have reduced or substantially eliminated expression of an endogenous MADS15 gene.

More specifically, the present invention provides a method for the production of transgenic plants having increased seed yield which method comprises:

-   -   introducing and expressing in a plant, plant part or plant cell         a gene construct comprising one or more control sequences         capable of preferentially driving expression of an inverted         repeat MADS15 nucleic acid sequence in a plant so as to silence         an endogenous MADS15 gene in the plant; and     -   cultivating the plant, plant part or plant cell under conditions         promoting plant growth and development.

Preferably, the construct introduced into a plant is one comprising an inverted repeat (in part or complete) of a MADS15 gene or fragment thereof, preferably capable of forming a hairpin structure.

According to a preferred feature of the present invention, the construct is introduced into a plant by transformation.

Generally after transformation, plant cells or cell groupings are selected for the presence of one or more markers which are encoded by plant-expressible genes co-transferred with the gene of interest, following which the transformed material is regenerated into a whole plant.

Following DNA transfer and regeneration, putatively transformed plants may be evaluated, for instance using Southern analysis, for the presence of the gene of interest, copy number and/or genomic organisation. Alternatively or additionally, expression levels of the newly introduced DNA may be monitored using Northern and/or Western analysis, or quantitative PCR, all techniques being well known to persons having ordinary skill in the art.

The generated transformed plants may be propagated by a variety of means, such as by clonal propagation or classical breeding techniques. For example, a first generation (or T1) transformed plant may be selfed to give homozygous second generation (or T2) transformants, and the T2 plants further propagated through classical breeding techniques.

The generated transformed organisms may take a variety of forms. For example, they may be chimeras of transformed cells and non-transformed cells; clonal transformants (e.g., all cells transformed to contain the expression cassette); grafts of transformed and untransformed tissues (e.g., in plants, a transformed rootstock grafted to an untransformed scion).

The present invention clearly extends to any plant cell or plant produced by any of the methods described herein, and to all plant parts and propagules thereof. The present invention extends further to encompass the progeny of a primary transformed or transfected cell, tissue, organ or whole plant that has been produced by any of the aforementioned methods, the only requirement being that progeny exhibit the same genotypic and/or phenotypic characteristic(s) as those produced by the parent in the methods according to the invention.

The invention also extends to harvestable parts of a plant such as seeds and products derived, preferably directly derived, from a harvestable part of such a plant, such as dry pellets or powders, oil, fat and fatty acids, starch or proteins.

The present invention also encompasses use of MADS15 nucleic acids for the reduction or substantial elimination of endogenous MADS15 gene expression in a plant for increasing plant seed yield as defined hereinabove.

Nucleic acids encoding the MADS15 protein described herein, or the MADS15 proteins themselves, may find use in breeding programmes in which a DNA marker is identified which may be genetically linked to a MADS15-encoding gene. The nucleic acids/genes, or the MADS15 proteins themselves may be used to define a molecular marker. This DNA or protein marker may then be used in breeding programmes to select plants having enhanced yield-related traits as defined hereinabove in the methods of the invention.

Allelic variants of a MADS15 protein-encoding nucleic acid/gene may also find use in marker-assisted breeding programmes. Such breeding programmes sometimes require introduction of allelic variation by mutagenic treatment of the plants, using for example EMS mutagenesis; alternatively, the programme may start with a collection of allelic variants of so called “natural” origin caused unintentionally. Identification of allelic variants then takes place, for example, by PCR. This is followed by a step for selection of superior allelic variants of the sequence in question and which give increased yield. Selection is typically carried out by monitoring growth performance of plants containing different allelic variants of the sequence in question. Growth performance may be monitored in a greenhouse or in the field. Further optional steps include crossing plants in which the superior allelic variant was identified with another plant. This could be used, for example, to make a combination of interesting phenotypic features.

Nucleic acids encoding MADS15 proteins may also be used as probes for genetically and physically mapping the genes that they are a part of, and as markers for traits linked to those genes. Such information may be useful in plant breeding in order to develop lines with desired phenotypes. Such use of MADS15 protein-encoding nucleic acids requires only a nucleic acid sequence of at least 15 nucleotides in length. The MADS15 protein-encoding nucleic acids may be used as restriction fragment length polymorphism (RFLP) markers. Southern blots (Sambrook J, Fritsch E F and Maniatis T (1989) Molecular Cloning, A Laboratory Manual) of restriction-digested plant genomic DNA may be probed with the MADS15 protein-encoding nucleic acids. The resulting banding patterns may then be subjected to genetic analyses using computer programs such as MapMaker (Lander et al. (1987) Genomics 1: 174-181) in order to construct a genetic map. In addition, the nucleic acids may be used to probe Southern blots containing restriction endonuclease-treated genomic DNAs of a set of individuals representing parent and progeny of a defined genetic cross. Segregation of the DNA polymorphisms is noted and used to calculate the position of the MADS15 protein-encoding nucleic acid in the genetic map previously obtained using this population (Botstein et al. (1980) Am. J. Hum. Genet. 32:314-331).

The production and use of plant gene-derived probes for use in genetic mapping is described in Bernatzky and Tanksley (1986) Plant Mol. Biol. Reporter 4: 37-41. Numerous publications describe genetic mapping of specific cDNA clones using the methodology outlined above or variations thereof. For example, F2 intercross populations, backcross populations, randomly mated populations, near isogenic lines, and other sets of individuals may be used for mapping. Such methodologies are well known to those skilled in the art.

The nucleic acid probes may also be used for physical mapping (i.e., placement of sequences on physical maps; see Hoheisel et al. In: Non-mammalian Genomic Analysis: A Practical Guide, Academic press 1996, pp. 319-346, and references cited therein).

In another embodiment, the nucleic acid probes may be used in direct fluorescence in situ hybridisation (FISH) mapping (Trask (1991) Trends Genet. 7:149-154). Although current methods of FISH mapping favour use of large clones (several kb to several hundred kb; see Laan et al. (1995) Genome Res. 5:13-20), improvements in sensitivity may allow performance of FISH mapping using shorter probes.

A variety of nucleic acid amplification-based methods for genetic and physical mapping may be carried out using the nucleic acids. Examples include allele-specific amplification (Kazazian (1989) J. Lab. Clin. Med. 11:95-96), polymorphism of PCR-amplified fragments (CAPS; Sheffield et al. (1993) Genomics 16:325-332), allele-specific ligation (Landegren et al. (1988) Science 241:1077-1080), nucleotide extension reactions (Sokolov (1990) Nucleic Acid Res. 18:3671), Radiation Hybrid Mapping (Walter et al. (1997) Nat. Genet. 7:22-28) and Happy Mapping (Dear and Cook (1989) Nucleic Acid Res. 17:6795-6807). For these methods, the sequence of a nucleic acid is used to design and produce primer pairs for use in the amplification reaction or in primer extension reactions. The design of such primers is well known to those skilled in the art. In methods employing PCR-based genetic mapping, it may be necessary to identify DNA sequence differences between the parents of the mapping cross in the region corresponding to the instant nucleic acid sequence. This, however, is generally not necessary for mapping methods.

The methods according to the present invention result in plants having enhanced yield-related traits, as described hereinbefore. These traits may also be combined with other economically advantageous traits, such as further yield-enhancing traits, tolerance to other abiotic and biotic stresses, traits modifying various architectural features and/or biochemical and/or physiological features.

Detailed Description of PLT

Surprisingly, it has now been found that increasing expression of a nucleic acid encoding a PLT transcription factor polypeptide gives plants having enhanced yield-related traits, in particular increased yield relative to control plants.

According to the present invention, there is provided a method for increasing plant yield relative to control plants, comprising increasing expression in a plant of a nucleic acid encoding a PLT transcription factor polypeptide.

The term “increased yield” as defined herein is taken to mean an increase in biomass (weight) of one or more parts of a plant, which may include aboveground (harvestable) parts and/or (harvestable) parts below ground.

In particular, such harvestable parts are seeds, and performance of the methods of the invention results in plants having increased seed yield relative to the seed yield of control plants.

Taking corn as an example, a yield increase may be manifested as one or more of the following: increase in the number of plants per hectare or acre, an increase in the number of ears per plant, an increase in the number of rows, number of kernels per row, kernel weight, thousand kernel weight, ear length/diameter, increase in the seed filling rate (which is the number of filled seeds divided by the total number of seeds and multiplied by 100), among others. Taking rice as an example, a yield increase may manifest itself as an increase in one or more of the following: number of plants per hectare or acre, number of panicles per plant, number of spikelets per panicle, number of flowers (florets) per panicle (which is expressed as a ratio of the number of filled seeds over the number of primary panicles), increase in the seed filling rate (which is the number of filled seeds divided by the total number of seeds and multiplied by 100), increase in thousand kernel weight, among others.

According to a preferred feature of the present invention, performance of the methods of the invention gives plants having increased seed yield relative to control plants. Therefore according to the present invention, there is provided a method for increasing seed yield in plants relative to the seed yield of control plants, the method comprising increasing expression in a plant of a nucleic acid encoding a PLT transcription factor polypeptide.

Since the transgenic plants according to the present invention have increased yield, it is likely that these plants exhibit an increased growth rate (during at least part of their life cycle), relative to the growth rate of corresponding wild type plants at a corresponding stage in their life cycle. The increased growth rate may be specific to one or more parts of a plant (including seeds), or may be throughout substantially the whole plant. A plant having an increased growth rate may even exhibit early flowering. The increase in growth rate may take place at one or more stages in the life cycle of a plant or during substantially the whole plant life cycle. Increased growth rate during the early stages in the life cycle of a plant may reflect enhanced vigour (increased seedling vigor at emergence). The increase in growth rate may alter the harvest cycle of a plant allowing plants to be sown later and/or harvested sooner than would otherwise be possible. If the growth rate is sufficiently increased, it may allow for the further sowing of seeds of the same plant species (for example sowing and harvesting of rice plants followed by sowing and harvesting of further rice plants all within one conventional growing period). Similarly, if the growth rate is sufficiently increased, it may allow for the further sowing of seeds of different plants species (for example the sowing and harvesting of corn plants followed by, for example, the sowing and optional harvesting of soy bean, potato or any other suitable plant). Harvesting additional times from the same rootstock in the case of some crop plants may also be possible. Altering the harvest cycle of a plant may lead to an increase in annual biomass production per acre (due to an increase in the number of times (say in a year) that any particular plant may be grown and harvested). An increase in growth rate may also allow for the cultivation of transgenic plants in a wider geographical area than their wild-type counterparts, since the territorial limitations for growing a crop are often determined by adverse environmental conditions either at the time of planting (early season) or at the time of harvesting (late season). Such adverse conditions may be avoided if the harvest cycle is shortened. The growth rate may be determined by deriving various parameters from growth curves, such parameters may be: T-Mid (the time taken for plants to reach 50% of their maximal size) and T-90 (time taken for plants to reach 90% of their maximal size), amongst others.

Performance of the methods of the invention gives plants having an increased growth rate. Therefore, according to the present invention, there is provided a method for increasing the growth rate of plants, which method comprises increasing expression in a plant of a nucleic acid encoding a PLT transcription factor polypeptide.

An increase in yield and/or growth rate occurs whether the plant is under non-stress conditions or whether the plant is exposed to various stresses compared to control plants. Plants typically respond to exposure to stress by growing more slowly. In conditions of severe stress, the plant may even stop growing altogether. Mild stress on the other hand is defined herein as being any stress to which a plant is exposed which does not result in the plant ceasing to grow altogether without the capacity to resume growth. Mild stress in the sense of the invention leads to a reduction in the growth of the stressed plants of less than 40%, 35% or 30%, preferably less than 25%, 20% or 15%, more preferably less than 14%, 13%, 12%, 11% or 10% or less in comparison to the control plant under non-stress conditions. Due to advances in agricultural practices (irrigation, fertilization, pesticide treatments) severe stresses are not often encountered in cultivated crop plants. As a consequence, the compromised growth induced by mild stress is often an undesirable feature for agriculture. Mild stresses are the everyday biotic and/or abiotic (environmental) stresses to which a plant is exposed. Abiotic stresses may be due to drought or excess water, anaerobic stress, salt stress, chemical toxicity, oxidative stress and hot, cold or freezing temperatures. The abiotic stress may be an osmotic stress caused by a water stress (particularly due to drought), salt stress, oxidative stress or an ionic stress. Biotic stresses are typically those stresses caused by pathogens, such as bacteria, viruses, fungi and insects.

In particular, the methods of the present invention may be performed under non-stress conditions or under conditions of mild drought to give plants having increased yield relative to control plants. As reported in Wang et al. (Planta (2003) 218: 1-14), abiotic stress leads to a series of morphological, physiological, biochemical and molecular changes that adversely affect plant growth and productivity. Drought, salinity, extreme temperatures and oxidative stress are known to be interconnected and may induce growth and cellular damage through similar mechanisms. Rabbani et al. (Plant Physiol (2003) 133: 1755-1767) describes a particularly high degree of “cross talk” between drought stress and high-salinity stress. For example, drought and/or salinisation are manifested primarily as osmotic stress, resulting in the disruption of homeostasis and ion distribution in the cell. Oxidative stress, which frequently accompanies high or low temperature, salinity or drought stress, may cause denaturing of functional and structural proteins. As a consequence, these diverse environmental stresses often activate similar cell signaling pathways and cellular responses, such as the production of stress proteins, up-regulation of anti-oxidants, accumulation of compatible solutes and growth arrest. The term “non-stress” conditions as used herein are those environmental conditions that allow optimal growth of plants. Persons skilled in the art are aware of normal soil conditions and climatic conditions for a given location.

Performance of the methods of the invention gives plants grown under non-stress conditions or under mild drought conditions enhanced yield-related traits relative to control plants grown under comparable conditions. Therefore, according to the present invention, there is provided a method for enhancing yield-related traits, in particular for increasing yield, in plants grown under non-stress conditions or under mild drought conditions, which method comprises increasing expression in a plant of a nucleic acid encoding a PLT transcription factor polypeptide.

The methods of the invention are advantageously applicable to any plant.

Plants that are particularly useful in the methods of the invention include all plants which belong to the superfamily Viridiplantae, in particular monocotyledonous and dicotyledonous plants including fodder or forage legumes, ornamental plants, food crops, trees or shrubs. According to a preferred embodiment of the present invention, the plant is a crop plant. Examples of crop plants include soybean, sunflower, canola, alfalfa, rapeseed, cotton, tomato, potato and tobacco. Examples of typical crop plants grown for oil production include soybean, sunflower, cotton, canola, peanuts or palm. Examples of typical crop plants grown for starch production include rice, wheat, barley, corn or potato. Further preferably, the plant is a monocotyledonous plant. Examples of monocotyledonous plants include sugarcane. More preferably the plant is a cereal. Examples of cereals include rice, maize, wheat, barley, millet, rye, triticale, sorghum and oats.

The term “PLT transcription factor polypeptide” as defined herein refers to any polypeptide comprising in increasing order of preference at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% sequence identity to the AP2 domain represented by SEQ ID NO: 191.

Preferably the PLT transcription factor polypeptide of choice is a PLT transcription factor polypeptide that in its natural genetic environment is essentially expressed in the roots (below ground parts) of the plant.

Further preferably, the PLT transcription factor polypeptide comprises either one motif but preferably both of motif1 as represented by SEQ ID NO: 192 PK(V/L)(A/E)DFLG and motif 2 as represented by SEQ ID NO: 209: (V/L)FX(M/V)WN(D/E), wherein X may be any amino acid; preferably motif 2 has the sequence of SEQ ID NO: 193 (V/L)F(T/S/N)(M/V)WN(D/E).

Examples of PLT transcription factor polypeptides comprising (i) in increasing order of preference at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% sequence identity to the AP2 domain represented by SEQ ID NO: 191 are proteins represented by the sequences given in Table I in the examples section. Preferred examples are represented by SEQ ID NO: 176 and SEQ ID NO: 178.

The AP2 domain in a PLT transcription factor polypeptide may be identified using specialised databases e.g. SMART (Schultz et al. (1998) Proc. Natl. Acad. Sci. USA 95, 5857-5864; Letunic et al. (2002) Nucleic Acids Res 30, 242-244), InterPro (Mulder et al., (2003) Nucl. Acids. Res. 31, 315-318), Prosite (Bucher and Bairoch (1994), A generalized profile syntax for biomolecular sequences motifs and its function in automatic sequence interpretation. (In) ISMB-94; Proceedings 2nd International Conference on Intelligent Systems for Molecular Biology. Altman R., Brutlag D., Karp P., Lathrop R., Searls D., Eds., pp 53-61, AAAIPress, Menlo Park; Hulo et al., Nucl. Acids. Res. 32:D134-D137, (2004)) or Pfam (Bateman et al., Nucleic Acids Research 30(1): 276-280 (2002)). The AP2 domain of a PLT transcription factor comprises two repeats R1 and R2, each of about 68 amino acids and separated by a linker region (FIG. 13).

The AP2 domain as represented by SEQ ID NO: 191 may be identified using methods for the alignment of sequences for comparison as described hereinabove. In some instances, the default parameters may be adjusted to modify the stringency of the search. For example using BLAST, the statistical significance threshold (called “expect” value) for reporting matches against database sequences may be increased to show less stringent matches. This way, short nearly exact matches may be identified, including motif1 as represented by SEQ ID NO: 192 and motif 2 as represented by SEQ ID NO: 209, preferably as represented by SEQ ID NO: 193.

Homologues of a PLT transcription factor polypeptide may also be used to perform the methods of invention. Homologues (or homologous proteins) may readily be identified using routine techniques well known in the art, such as by sequence alignment. Methods for the alignment of sequences for comparison are well known in the art, such methods include GAP, BESTFIT, BLAST, FASTA and TFASTA. GAP uses the algorithm of Needleman and Wunsch ((1970) J Mol Biol 48: 443-453) to find the alignment of two complete sequences that maximizes the number of matches and minimizes the number of gaps. The BLAST algorithm (Altschul et al. (1990) J Mol Biol 215: 403-10) calculates percent sequence identity and performs a statistical analysis of the similarity between the two sequences. The software for performing BLAST analysis is publicly available through the National Centre for Biotechnology Information. Homologues may readily be identified using, for example, the ClustalW multiple sequence alignment algorithm (version 1.83), with the default pairwise alignment parameters, and a scoring method in percentage. Minor manual editing may be performed to optimise alignment between conserved motifs, as would be apparent to a person skilled in the art.

Homologues also include orthologues and paralogues. Orthologues and paralogues may easily be found by performing a so-called reciprocal blast search. This may be done by a first BLAST involving BLASTing a query sequence (for example, SEQ ID NO: 175, SEQ ID NO: 176, SEQ ID NO: 177 or SEQ ID NO: 178) against any sequence database, such as the publicly available NCBI database. BLASTN or TBLASTX (using standard default values) may be used when starting from a nucleotide sequence and BLASTP or TBLASTN (using standard default values) may be used when starting from a protein sequence. The BLAST results may optionally be filtered. The full-length sequences of either the filtered results or non-filtered results are then BLASTed back (second BLAST) against sequences from the organism from which the query sequence is derived (where the query sequence is SEQ ID NO: 175, SEQ ID NO: 176, SEQ ID NO: 177 or SEQ ID NO: 178, the second BLAST would therefore be against Arabidopsis thaliana sequences). The results of the first and second BLASTs are then compared. A paralogue is identified if a high-ranking hit from the first BLAST is from the same species as from which the query sequence is derived; an orthologue is identified if a high-ranking hit is not from the same species as from which the query sequence is derived. High-ranking hits are those having a low E-value. The lower the E-value, the more significant the score (or in other words the lower the chance that the hit was found by chance). Computation of the E-value is well known in the art. In the case of large families, ClustalW may be used, followed by a neighbour joining tree, to help visualize clustering of related genes and to identify orthologues and paralogues. In addition to E-values, comparisons are also scored by percentage identity. Percentage identity refers to the number of identical nucleotides (or amino acids) between the two compared nucleic acid (or polypeptide) sequences over a particular length. PLT transcription factor polypeptide homologues have in increasing order of preference at least 25%, 30%, 40%, 50%, 60%, 70%, 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% or more sequence identity or similarity (functional identity) to an unmodified PLT transcription factor polypeptide as represented by SEQ ID NO: 176 or SEQ ID NO: 178. Percentage identity between PLT transcription factor polypeptide homologues outside of the AP2 domain is reputedly low. Preferably, PLT transcription factor polypeptide homologues comprise an AP2 domain with in increasing order of preference at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% sequence identity to the AP2 domain represented by SEQ ID NO: 191. Further preferably, PLT transcription factor polypeptide homologues are as represented by SEQ ID NO: 180, SEQ ID NO: 182, SEQ ID NO: 184, SEQ ID NO: 186, SEQ ID NO: 188, SEQ ID NO: 200 and SEQ ID NO: 202.

The PLT polypeptide may be a derivative of SEQ ID NO: 176 or SEQ ID NO: 178. “Derivatives” include peptides, oligopeptides, polypeptides which may, compared to the amino acid sequence of the naturally-occurring form of the protein, such as the one presented in SEQ ID NO: 176 or SEQ ID NO: 178, comprise substitutions of amino acids with non-naturally occurring amino acid residues, or additions of non-naturally occurring amino acid residues. Derivatives of SEQ ID NO: 180, SEQ ID NO: 182, SEQ ID NO: 184, SEQ ID NO: 186, SEQ ID NO: 188, SEQ ID NO: 200 and SEQ ID NO: 202 are further examples which may be suitable for use in the methods of the invention provided that they have the same or similar biological activity.

Furthermore, PLT transcription factor polypeptides (at least in their native form) typically have DNA-binding activity and an activation domain. A person skilled in the art may easily determine the presence of an activation domain and DNA-binding activity using routine techniques and procedures. Proteins interacting with PLT transcription factor polypeptides (as, for example, in transcriptional complexes) may easily be identified using standard techniques for a person skilled in the art.

Examples of nucleic acids encoding PLT transcription factor polypeptides include but are not limited to those represented by any one of: SEQ ID NO: 175, SEQ ID NO: 177, SEQ ID NO: 179, SEQ ID NO: 181, SEQ ID NO: 183, SEQ ID NO: 185, SEQ ID NO: 187, SEQ ID NO: 199 and SEQ ID NO: 201. Variants of nucleic acids encoding PLT transcription factor polypeptides may be suitable for use in the methods of the invention provided that they have the same or similar biological activity. Suitable variants include portions of nucleic acids encoding PLT transcription factor polypeptides and/or nucleic acids capable of hybridising with nucleic acids/genes encoding PLT transcription factor polypeptides. Further variants include splice variants and allelic variants of nucleic acids encoding PLT transcription factor polypeptides.

The term “portion” as defined herein refers to a piece of DNA encoding a polypeptide comprising in increasing order of preference at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% sequence identity to the AP2 domain represented by SEQ ID NO: 191. The portion may further comprise either one motif but preferably both of motif1 as represented by SEQ ID NO: 192 and/or motif 2 as represented by SEQ ID NO: 209; preferably, motif 2 has the sequences as represented by SEQ ID NO: 193.

A portion may be prepared, for example, by making one or more deletions to a nucleic acid encoding a PLT transcription factor polypeptide. The portions may be used in isolated form or they may be fused to other coding (or non coding) sequences in order to, for example, produce a protein that combines several activities. When fused to other coding sequences, the resulting polypeptide produced upon translation may be bigger than that predicted for the PLT transcription factor portion. Preferably, the portion codes for a polypeptide with substantially the same biological activity as the PLT transcription factor polypeptides of SEQ ID NO: 176 and SEQ ID NO: 178.

Preferably, the portion is a portion of a nucleic acid as represented by any one of the sequences listed in Table I of the Examples. Most preferably the portion is a portion of a nucleic acid as represented by SEQ ID NO: 175 and SEQ ID NO: 177.

Another variant of a nucleic acid encoding a PLT transcription factor polypeptide, useful in the methods of the present invention, is a nucleic acid capable of hybridising under reduced stringency conditions, preferably under stringent conditions, with a probe derived from the nucleic acid as defined hereinbefore, which hybridising sequence encodes a polypeptide comprising in increasing order of preference at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% sequence identity to the AP2 domain represented by SEQ ID NO: 191. The hybridizing sequence may further comprise either one motif but preferably both of motif1 as represented by SEQ ID NO: 192 and/or motif 2 as represented by SEQ ID NO: 209, preferably as represented by SEQ ID NO: 193.

Preferably, the hybridising sequence is one that is capable of hybridising to a nucleic acid as represented by (or to probes derived from) any one of the sequences listed in Table I of the Examples, or to a portion of any of the aforementioned sequences (the target sequence). Most preferably the hybridising sequence is capable of hybridising to SEQ ID NO: 175 or to SEQ ID NO: 177 (or to probes derived therefrom). Probes are generally less than 1000 bp in length, preferably less than 500 bp in length. Commonly, probe lengths for DNA-DNA hybridisations such as Southern blotting, vary between 100 and 500 bp, whereas the hybridising region in probes for DNA-DNA hybridisations such as in PCR amplification generally are shorter than 50 but longer than 10 nucleotides.

The PLT transcription factor polypeptide may be encoded by a splice variant. The term “splice variant” as used herein encompasses variants of a nucleic acid sequence in which selected introns and/or exons have been excised, replaced, displaced or added, or in which introns have been shortened or lengthened. Such variants will be ones in which the substantial biological activity of the protein is retained, which may be achieved by selectively retaining functional segments of the protein. Such splice variants may be found in nature or may be manmade. Methods for making such splice variants are well known in the art.

Preferred splice variants are splice variants of the nucleic acid encoding a PLT transcription factor polypeptide comprising in increasing order of preference at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% sequence identity to the AP2 domain represented by SEQ ID NO: 191. Splice variants may further comprise either one motif but preferably both of motif1 as represented by SEQ ID NO: 192 and/or motif 2 as represented by SEQ ID NO: 209, preferably as represented by SEQ ID NO: 193.

Further preferred splice variants of nucleic acids encoding PLT transcription factor polypeptides comprising features as defined hereinabove are splice variants of a nucleic acid as represented by any one of the sequences listed in Table I of the Examples. Most preferred is a splice variant of a nucleic acid sequence as represented by SEQ ID NO: 175 and SEQ ID NO: 177.

The PLT transcription factor polypeptide may also be encoded by an allelic variant of a nucleic acid encoding a polypeptide comprising from comprising in increasing order of preference at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% sequence identity to the AP2 domain represented by SEQ ID NO: 191. The allelic variant may further comprise either one motif but preferably both of motif1 as represented by SEQ ID NO: 192 and/or motif 2 as represented by SEQ ID NO: 209, preferably as represented by SEQ ID NO: 193.

Preferred allelic variants of nucleic acids encoding PLT transcription factor polypeptides comprising features as defined hereinabove are splice variants of a nucleic acid as represented by any one of the sequences listed in Table I of the Examples. Most preferred is an allelic variant of a nucleic acid sequence as represented by SEQ ID NO: 175 and SEQ ID NO: 177.

The increase in expression of a nucleic acid encoding a PLT transcription factor polypeptide leads to raised corresponding mRNA or polypeptide levels, which could equate to raised activity of the PLT transcription factor polypeptide; or the activity may also be raised when there is no change in polypeptide levels, or even when there is a reduction in polypeptide levels. This may occur when the intrinsic properties of the polypeptide are altered, for example, by making mutant versions that are more active that the wild type polypeptide.

Directed evolution (or gene shuffling) may be used to generate variants of nucleic acids encoding PLT transcription factor polypeptides. This consists of iterations of DNA shuffling followed by appropriate screening and/or selection to generate variants of nucleic acids or portions thereof encoding PLT transcription factor polypeptides or homologues or portions thereof having an modified biological activity (Castle et al., (2004) Science 304(5674): 1151-4; U.S. Pat. Nos. 5,811,238 and 6,395,547).

Site-directed mutagenesis may be used to generate variants of nucleic acids encoding PLT transcription factor polypeptides. Several methods are available to achieve site-directed mutagenesis, the most common being PCR based methods (current protocols in molecular biology. Wiley Eds.).

Directed evolution and site-directed mutagenesis are examples of technologies that enable the generation of variants of nucleic acids encoding PLT transcription factor polypeptides with modified activity useful to perform the methods of the invention.

Nucleic acids encoding PLT transcription factor polypeptides may be derived from any natural or artificial source. The nucleic acid may be modified from its native form in composition and/or genomic environment through deliberate human manipulation. Preferably the PLT transcription factor nucleic acid is from a plant, preferably from a dicotyledonous plant, further preferably from the Brassicaceae family, more preferably from the Arabidopsis genus, most preferably the nucleic acid is from Arabidopsis thaliana.

The methods of the invention rely on increased expression of a nucleic acid encoding a PLT transcription factor polypeptide in a plant. The nucleic acid may be a full-length nucleic acid or may be a portion or a hybridising sequence or another nucleic acid variant as hereinbefore defined.

The methods of the invention rely on increased expression of a nucleic acid encoding a PLT transcription factor polypeptide in a plant.

The invention also provides genetic constructs and vectors to facilitate introduction and/or expression in a plant of the nucleic acid sequences useful in the methods according to the invention.

Therefore, there is provided a gene construct comprising:

-   -   (i) A nucleic acid encoding a PLT transcription factor         polypeptide as defined hereinabove;     -   (ii) One or more control sequences, of which at least one is a         medium strength constitutive promoter.

Constructs useful in the methods according to the present invention may be constructed using recombinant DNA technology well known to persons skilled in the art. The gene constructs may be inserted into vectors, which may be commercially available, suitable for transforming into plants and suitable for expression of the gene of interest in the transformed cells. The invention therefore provides use of a gene construct as defined hereinabove in the methods of the invention.

Plants are transformed with a vector comprising the sequence of interest (i.e., a nucleic acid encoding a PLT transcription factor polypeptide). The skilled artisan is well aware of the genetic elements that must be present on the vector in order to successfully transform, select and propagate host cells containing the sequence of interest. The sequence of interest is operably linked to one or more control sequences (at least to a promoter).

The nucleic acid encoding a PLT transcription factor polypeptide or variant thereof is operably linked to a constitutive promoter, preferably a medium strength constitutive promoter. A constitutive promoter is transcriptionally active during most, but not necessarily all, phases of its growth and development and is substantially ubiquitously expressed at moderate levels. Promoter strength and/or expression pattern can be analysed as described in the definitions section. The promoter strength and/or expression pattern can for example be compared to that of a well-characterised shoot preferred reference promoter, such as the Cab27 promoter (weak expression, GenBank AP004700) or the putative protochlorophyllid reductase promoter (strong expression, GenBank AL606456). Preferably the promoter used in the methods of the present invention is derived from a plant, further preferably a monocotyledonous plant. Most preferred is use of a GOS2 promoter (from rice) (SEQ ID NO: 194 or alternatively SEQ ID NO: 210). It should be clear that the applicability of the present invention is not restricted to the nucleic acid represented by SEQ ID NO: 175 or SEQ ID NO: 177, nor is the applicability of the invention restricted to expression of a nucleic acid encoding a PLT transcription factor polypeptide when driven by a GOS2 promoter. Examples of other constitutive promoters that may also be used to drive expression of a nucleic acid encoding a PLT transcription factor polypeptide are shown in the definitions section.

Optionally, one or more terminator sequences (also a control sequence) may be used in the construct introduced into a plant. Additional regulatory elements may include transcriptional as well as translational enhancers. Those skilled in the art will be aware of terminator and enhancer sequences that may be suitable for use in performing the invention. Other control sequences (besides promoter, enhancer, silencer, intron sequences, 3′UTR and/or 5′UTR regions) may be protein and/or RNA stabilizing elements. Such sequences would be known or may readily be obtained by a person skilled in the art.

The genetic constructs of the invention may further include an origin of replication sequence that is required for maintenance and/or replication in a specific cell type. One example is when a genetic construct is required to be maintained in a bacterial cell as an episomal genetic element (e.g. plasmid or cosmid molecule). Preferred origins of replication include, but are not limited to, the f1-ori and colE1. The genetic construct may optionally comprise a selectable marker gene.

The present invention also encompasses plants obtainable by the methods according to the present invention. The present invention therefore provides plants, plant parts or plant cells thereof obtainable by the method according to the present invention, which plants or parts or cells thereof comprise a nucleic acid transgene encoding a PLT transcription factor polypeptide under the control of a constitutive promoter, preferably a non-viral constitutive promoter.

The invention also provides a method for the production of transgenic plants having increased yield relative to control plants, comprising introduction and preferential expression of a nucleic acid encoding a PLT transcription factor polypeptide in a plant.

More specifically, the present invention provides a method for the production of transgenic plants having increased yield which method comprises:

-   -   (i) introducing and expressing a nucleic acid encoding a PLT         transcription factor polypeptide in a plant; and     -   (ii) cultivating the plant cell under conditions promoting plant         growth and development.

The nucleic acid may be introduced directly into a plant cell or into the plant itself (including introduction into a tissue, organ or any other part of a plant). According to a preferred feature of the present invention, the nucleic acid is preferably introduced into a plant by transformation.

Generally after transformation, plant cells or cell groupings are selected for the presence of one or more markers which are encoded by plant-expressible genes co-transferred with the gene of interest, following which the transformed material is regenerated into a whole plant. Following DNA transfer and regeneration, putatively transformed plants may be evaluated, for instance using Southern analysis, for the presence of the gene of interest, copy number and/or genomic organisation. Alternatively or additionally, expression levels of the newly introduced DNA may be monitored using Northern and/or Western analysis, or quantitative PCR, all techniques being well known to persons having ordinary skill in the art.

The generated transformed plants may be propagated by a variety of means, such as by clonal propagation or classical breeding techniques. For example, a first generation (or T1) transformed plant may be selfed to give homozygous second generation (or T2) transformants, and the T2 plants further propagated through classical breeding techniques.

The generated transformed organisms may take a variety of forms. For example, they may be chimeras of transformed cells and non-transformed cells; clonal transformants (e.g., all cells transformed to contain the expression cassette); grafts of transformed and untransformed tissues (e.g., in plants, a transformed rootstock grafted to an untransformed scion).

The present invention clearly extends to any plant cell or plant produced by any of the methods described herein, and to all plant parts and propagules thereof. The present invention extends further to encompass the progeny of a primary transformed or transfected cell, tissue, organ or whole plant that has been produced by any of the aforementioned methods, the only requirement being that progeny exhibit the same genotypic and/or phenotypic characteristic(s) as those produced by the parent in the methods according to the invention.

The invention also includes host cells containing an isolated nucleic acid encoding a PLT transcription factor polypeptide. Preferred host cells according to the invention are plant cells.

The invention furthermore extends to harvestable parts of a plant such as, but not limited to seeds, leaves, fruits, flowers, stems, rhizomes, tubers and bulbs. The invention furthermore relates to products derived, preferably directly derived, from a harvestable part of such a plant, such as dry pellets or powders, oil, fat and fatty acids, starch or proteins.

The present invention also encompasses use of nucleic acids encoding PLT transcription factor polypeptides and use of PLT transcription factor polypeptides in increasing plant yield as defined hereinabove in the methods of the invention.

The increased expression of a nucleic acid encoding a PLT transcription factor polypeptide may be performed by introducing a genetic modification (preferably in the locus of a PLT transcription factor gene). The locus of a gene as defined herein is taken to mean a genomic region, which includes the gene of interest and 10 KB up- or downstream of the coding region.

The genetic modification may be introduced by alternative methods as the one described hereinabove, for example, by any one (or more) of the following: T-DNA activation, TILLING and homologous recombination. Following introduction of the genetic modification, there follows an optional step of selecting for increased expression of a nucleic acid encoding a PLT transcription factor polypeptide, which increased expression gives plants having increased yield.

T-DNA activation tagging results in transgenic plants that show dominant phenotypes due to modified expression of genes close to the introduced promoter. The promoter to be introduced a medium stength constitutive promoter capable of increasing expression of the nucleic acid encoding a PLT transcription factor polypeptide in a plant.

A genetic modification may also be introduced in the locus of a gene encoding a PLT transcription factor polypeptide using the technique of TILLING (Targeted Induced Local Lesions In Genomes).

The effects of the invention may also be reproduced using homologous recombination. The nucleic acid to be introduced (which may be a nucleic acid encoding a PLT transcription factor polypeptide or variant thereof as hereinbefore defined) is targeted to the locus of a PLT gene.

The nucleic acid to be targeted may be an improved allele used to replace the endogenous gene or may be introduced in addition to the endogenous gene.

T-DNA activation, TILLING and homologous recombination are examples of technologies that enable the generation of genetic modifications comprising increasing expression of a nucleic acid encoding a PLT transcription factor polypeptide in plants.

Nucleic acids encoding PLT transcription factor polypeptides, or PLT transcription factor polypeptides, may find use in breeding programmes in which a DNA marker is identified which may be genetically linked to a PLT transcription factor gene. The nucleic acids/genes, or the PLT transcription factor polypeptides may be used to define a molecular marker. This DNA or protein marker may then be used in breeding programmes to select plants having increased yield as defined hereinabove in the methods of the invention.

Allelic variants of a PLT transcription factor nucleic acid/gene may also find use in marker-assisted breeding programmes. Such breeding programmes sometimes require introduction of allelic variation by mutagenic treatment of the plants, using for example EMS mutagenesis; alternatively, the programme may start with a collection of allelic variants of so called “natural” origin caused unintentionally. Identification of allelic variants then takes place, for example, by PCR. This is followed by a step for selection of superior allelic variants of the sequence in question and which give increased yield. Selection is typically carried out by monitoring growth performance of plants containing different allelic variants of the sequence in question. Growth performance may be monitored in a greenhouse or in the field. Further optional steps include crossing plants in which the superior allelic variant was identified with another plant. This could be used, for example, to make a combination of interesting phenotypic features.

A nucleic acid encoding a PLT transcription factor polypeptide may also be used as probes for genetically and physically mapping the genes that they are a part of, and as markers for traits linked to those genes. Such information may be useful in plant breeding in order to develop lines with desired phenotypes. Such use of PLT transcription factor nucleic acids requires only a nucleic acid sequence of at least 15 nucleotides in length. The PLT transcription factor nucleic acids may be used as restriction fragment length polymorphism (RFLP) markers. Southern blots (Sambrook J, Fritsch E F and Maniatis T (1989) Molecular Cloning, A Laboratory Manual) of restriction-digested plant genomic DNA may be probed with the PLT transcription factor nucleic acids. The resulting banding patterns may then be subjected to genetic analyses using computer programs such as MapMaker (Lander et al. (1987) Genomics 1: 174-181) in order to construct a genetic map. In addition, the nucleic acids may be used to probe Southern blots containing restriction endonuclease-treated genomic DNAs of a set of individuals representing parent and progeny of a defined genetic cross. Segregation of the DNA polymorphisms is noted and used to calculate the position of the PLT transcription factor nucleic acid in the genetic map previously obtained using this population (Botstein et al. (1980) Am. J. Hum. Genet. 32:314-331).

The production and use of plant gene-derived probes for use in genetic mapping is described in Bernatzky and Tanksley (1986) Plant Mol. Biol. Reporter 4: 37-41. Numerous publications describe genetic mapping of specific cDNA clones using the methodology outlined above or variations thereof. For example, F2 intercross populations, backcross populations, randomly mated populations, near isogenic lines, and other sets of individuals may be used for mapping. Such methodologies are well known to those skilled in the art.

The nucleic acid probes may also be used for physical mapping (i.e., placement of sequences on physical maps; see Hoheisel et al. In: Non-mammalian Genomic Analysis: A Practical Guide, Academic press 1996, pp. 319-346, and references cited therein).

In another embodiment, the nucleic acid probes may be used in direct fluorescence in situ hybridisation (FISH) mapping (Trask (1991) Trends Genet. 7:149-154). Although current methods of FISH mapping favor use of large clones (several kb to several hundred kb; see Laan et al. (1995) Genome Res. 5:13-20), improvements in sensitivity may allow performance of FISH mapping using shorter probes.

A variety of nucleic acid amplification-based methods for genetic and physical mapping may be carried out using the nucleic acids. Examples include allele-specific amplification (Kazazian (1989) J. Lab. Clin. Med. 11:95-96), polymorphism of PCR-amplified fragments (CAPS; Sheffield et al. (1993) Genomics 16:325-332), allele-specific ligation (Landegren et al. (1988) Science 241:1077-1080), nucleotide extension reactions (Sokolov (1990) Nucleic Acid Res. 18:3671), Radiation Hybrid Mapping (Walter et al. (1997) Nat. Genet. 7:22-28) and Happy Mapping (Dear and Cook (1989) Nucleic Acid Res. 17:6795-6807). For these methods, the sequence of a nucleic acid is used to design and produce primer pairs for use in the amplification reaction or in primer extension reactions. The design of such primers is well known to those skilled in the art. In methods employing PCR-based genetic mapping, it may be necessary to identify DNA sequence differences between the parents of the mapping cross in the region corresponding to the instant nucleic acid sequence. This, however, is generally not necessary for mapping methods.

The methods according to the present invention result in plants having increased yield, as described hereinbefore. This increased yield may also be combined with other economically advantageous traits, such as further yield-enhancing traits, tolerance to other abiotic and biotic stresses, traits modifying various architectural features and/or biochemical and/or physiological features.

Detailed Description of bHLH

Surprisingly, it has now been found that modulating expression in a plant of a nucleic acid encoding a particular class of bHLH transcription factor gives plants having enhanced yield-related traits relative to control plants. The particular class of bHLH transcription factor suitable for enhancing yield-related traits in plants is described in detail below.

The present invention provides a method for enhancing yield-related traits in plants relative to control plants, comprising modulating expression in a plant of a nucleic acid encoding a particular class of bHLH transcription factor.

A preferred method for modulating (preferably, increasing) expression of a nucleic acid encoding a bHLH transcription factor is by introducing and expressing in a plant a nucleic acid encoding a particular class of bHLH transcription factor as further defined below.

The nucleic acid to be introduced into a plant (and therefore useful in performing the methods of the invention) is any nucleic acid encoding the type of bHLH transcription factor which will now be described. A bHLH transcription factor as defined herein refers to a polypeptide represented by any one of SEQ ID NO 213, SEQ ID NO 215, SEQ ID NO: 217, SEQ ID NO: 219, SEQ ID NO 225, SEQ ID NO: 297, SEQ ID NO: 299 and SEQ ID NO: 301. The invention is illustrated by transforming plants with the Oryza sativa sequence represented by SEQ ID NO: 212, encoding the polypeptide of SEQ ID NO: 213. SEQ ID NO: 215 from Oryza sativa (encoded by SEQ ID NO: 214) and SEQ ID NO: 217 from Oryza sativa (encoded by SEQ ID NO: 216) are paralogues of the polypeptide of SEQ ID NO: 213. SEQ ID NO: 219 from Arabidopsis thaliana (encoded by SEQ ID NO: 218) and SEQ ID NO: 225 from Arabidopsis thaliana (encoded by SEQ ID NO: 224) are orthologues of the polypeptide of SEQ ID NO: 213. SEQ ID NO: 221 from Arabidopsis thaliana (encoded by SEQ ID NO: 220) and SEQ ID NO: 223 from Arabidopsis thaliana (encoded by SEQ ID NO: 222) are variants of SEQ ID NO: 218 and SEQ ID NO: 219.

Orthologues and paralogues may easily be found by performing a so-called reciprocal blast search. Typically this involves a first BLAST involving BLASTing a query sequence (for example, SEQ ID NO: 212, SEQ ID NO: 213, SEQ ID NO: 214, SEQ ID NO: 215, SEQ ID NO: 216, SEQ ID NO: 217, SEQ ID NO: 218, SEQ ID NO: 219, SEQ ID NO: 224 or SEQ ID NO: 225) against any sequence database, such as the publicly available NCBI database. BLASTN or TBLASTX (using standard default values) are generally used when starting from a nucleotide sequence, and BLASTP or TBLASTN (using standard default values) when starting from a protein sequence. The BLAST results may optionally be filtered. The full-length sequences of either the filtered results or non-filtered results are then BLASTed back (second BLAST) against sequences from the organism from which the query sequence is derived (where the query sequence is SEQ ID NO: 212, SEQ ID NO: 213, SEQ ID NO: 214, SEQ ID NO: 215, SEQ ID NO: 216 or SEQ ID NO: 217, the second BLAST would therefore be against Oryza sequences; where the query sequence is SEQ ID NO: 218, SEQ ID NO: 219, SEQ ID NO: 224 or SEQ ID NO: 225, the second BLAST would therefore be against Arabidopsis sequences). The results of the first and second BLASTs are then compared. A paralogue is identified if a high-ranking hit from the first blast is from the same species as from which the query sequence is derived, a BLAST back then ideally results in the query sequence as highest hit; an orthologue is identified if a high-ranking hit in the first BLAST is not from the same species as from which the query sequence is derived, and preferably results upon BLAST back in the query sequence being among the highest hits.

High-ranking hits are those having a low E-value. The lower the E-value, the more significant the score (or in other words the lower the chance that the hit was found by chance). Computation of the E-value is well known in the art. In addition to E-values, comparisons are also scored by percentage identity. Percentage identity refers to the number of identical nucleotides (or amino acids) between the two compared nucleic acid (or polypeptide) sequences over a particular length. Preferably the score is greater than 50, more preferably greater than 100; and preferably the E-value is less than e-5, more preferably less than e-6. An example detailing the identification of orthologues and paralogues is given in Example 31 and Example 30 respectively herein. In the case of large families, ClustalW may be used, followed by a neighbour joining tree, to help visualize clustering of related genes and to identify orthologues and paralogues.

Examples of orthologues obtained by the BLAST procedure mentioned above are SEQ ID NO: 227 from Medicago truncatula (encoded by SEQ ID NO: 226) and SEQ ID NO: 229 from Hordeum vulgare (encoded by SEQ ID NO: 228). Further orthologues and paralogues may readily be identified using the BLAST procedure described above and by following the procedure given in the Examples section.

The proteins represented by SEQ ID NO: 297, 299 and 301 were hitherto unknown. Therefore, the invention also provides hitherto unknown bHLH transcription factors and bHLH transcription factor-encoding nucleic acids.

According to a further embodiment of the present invention, there is therefore provided an isolated nucleic acid molecule comprising:

-   -   (i) a nucleic acid represented by any one of SEQ ID NO: 296, SEQ         ID NO: 298 and SEQ ID NO: 300;     -   (ii) the complement of a nucleic acid represented by any one of         SEQ ID NO: 296, SEQ ID NO: 298 and SEQ ID NO: 300;     -   (iii) a nucleic acid encoding a bHLH transcription factor         having (a) in increasing order of preference, at least 50%, 55%,         60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or         more sequence identity to the amino acid sequence represented by         any one of SEQ ID NO: 297, SEQ ID NO: 299 and SEQ ID NO: 301,         and (b) a bHLH domain.

According to a further embodiment of the present invention, there is also provided an isolated polypeptide comprising:

-   -   (i) an amino acid sequence represented by any one of SEQ ID NO:         297, SEQ ID NO: 299 and SEQ ID NO: 301;     -   (ii) an amino acid sequence having (a) in increasing order of         preference, at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%,         90%, 95%, 96%, 97%, 98%, 99% or more sequence identity to any         one of the amino acid sequences represented by SEQ ID NO: 297,         SEQ ID NO: 299 and SEQ ID NO: 301, and (b) a bHLH domain;     -   (iii) derivatives of any of the amino acid sequences given         in (i) or (ii) above.

The polypeptides represented by any one of SEQ ID NO 213, SEQ ID NO 215, SEQ ID NO: 217, SEQ ID NO: 219, SEQ ID NO 221, SEQ ID NO 223, SEQ ID NO 225, SEQ ID NO: 227, SEQ ID NO: 229, SEQ ID NO: 297, SEQ ID NO: 299, SEQ ID NO: 301, or orthologues or paralogues of any of the aforementioned SEQ ID NOs, all comprise a bHLH domain.

bHLH domains are well known in the art and may readily be identified by persons skilled in the art. The family is defined by a bHLH signature domain, which consists of 60 or so amino acids with two functionally distinct regions. A basic region, located at the N-terminal end of the domain, is involved in DNA binding and consists of 15 or so amino acids with a high number of basic residues. An HLH region, at the C-terminal end, functions as a dimerization domain and mainly comprises hydrophobic residues that form two amphipathic helices separated by a loop region of variable sequence and length.

A bHLH domain may be identified using methods for the alignment of sequences for comparison. In some instances, default parameters may be adjusted to modify the stringency of the search. For example using BLAST, the statistical significance threshold (called E-value) for reporting matches against database sequences may be increased to show less stringent matches. In this way, short nearly exact matches may be identified.

Methods for the alignment of sequences for comparison are well known in the art, such methods include GAP, BESTFIT, BLAST, FASTA and TFASTA. GAP uses the algorithm of Needleman and Wunsch ((1970) J Mol Biol 48: 443-453) to find the global (over the whole the sequence) alignment of two sequences that maximizes the number of matches and minimizes the number of gaps. The BLAST algorithm (Altschul et al. (1990) J Mol Biol 215: 403-10) calculates percent sequence identity and performs a statistical analysis of the similarity between the two sequences. The software for performing BLAST analysis is publicly available through the National Centre for Biotechnology Information (NCBI). Homologues may readily be identified using, for example, the ClustalW multiple sequence alignment algorithm (version 1.83), with the default pairwise alignment parameters, and a scoring method in percentage. Minor manual editing may be performed to optimise alignment between conserved motifs, as would be apparent to a person skilled in the art.

Specialist databases also exist for the identification of domains. The bHLH domain in a bHLH transcription factor may be identified using, for example, SMART (Schultz et al. (1998) Proc. Natl. Acad. Sci. USA 95, 5857-5864; Letunic et al. (2002) Nucleic Acids Res 30, 242-244), InterPro (Mulder et al., (2003) Nucl. Acids. Res. 31, 315-318), Prosite (Bucher and Bairoch (1994), A generalized profile syntax for biomolecular sequences motifs and its function in automatic sequence interpretation. (In) ISMB-94; Proceedings 2nd International Conference on Intelligent Systems for Molecular Biology. Altman R., Brutlag D., Karp P., Lathrop R., Searls D., Eds., pp 53-61, AAAIPress, Menlo Park; Hulo et al., Nucl. Acids. Res. 32:D134-D137, (2004)) or Pfam (Bateman et al., Nucleic Acids Research 30(1): 276-280 (2002)). The HLH domain structure in the InterPro database is designated IPR001092 and IPR011598; PF00010 in the Pfam database; SM00353 in the SMART database and PS50888 in the PROSITE database. Furthermore, the alignment shown in FIG. 18 highlights the bHLH domain of bHLH transcription factors useful in the methods of the invention.

The polypeptides represented by any one of SEQ ID NO 213, SEQ ID NO 215, SEQ ID NO: 217, SEQ ID NO: 219, SEQ ID NO 225, SEQ ID NO: 297, SEQ ID NO: 299, SEQ ID NO: 301 or orthologues or paralogues of any of the aforementioned SEQ ID NOs, typically exhibit considerable sequence divergence outside of the conserved bHLH domain.

FIG. 19 a is a matrix showing the overall similarities and identities (in bold) of the bHLH type proteins described above. Even though the identities appear to be relatively low, polypeptides having sequence identity falling within the ranges shown in the matrix may be taken to be orthologues or paralogues of any of SEQ ID NO 213, SEQ ID NO 215, SEQ ID NO: 217, SEQ ID NO: 219 or SEQ ID NO 225; this may be confirmed by the reciprocal blast procedure described above. Typically, nucleic acids encoding bHLH transcription factors useful in the methods of the invention have, in increasing order of preference, at least 13%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95% or more sequence identity to the bHLH transcription factors represented by any one of SEQ ID NO 213, SEQ ID NO 215, SEQ ID NO: 217, SEQ ID NO: 219 or SEQ ID NO 225.

The matrix shown in FIG. 19 b shows similarities and identities (in bold) over the bHLH domain, where of course the values are higher than when considering full length proteins. Typically, nucleic acids encoding bHLH transcription factors useful in the methods of the invention have bHLH domains having, in increasing order of preference, at least 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95% or more sequence identity to the bHLH domain of any one of the polypeptides represented by any one of SEQ ID NO 213, SEQ ID NO 215, SEQ ID NO: 217, SEQ ID NO: 219 or SEQ ID NO 225.

A pattern of amino acids, termed a 5-9-13 configuration, may be found at three positions within the basic region of the bHLH domain (see FIG. 4 of Heim et al., 2003 (Mol. Biol. Evol. 20(5):735-747) and FIG. 18 herein where three upwardly pointing arrows show the configuration). The polypeptides represented by any one of SEQ ID NO 213, SEQ ID NO 215, SEQ ID NO: 217, SEQ ID NO: 219, SEQ ID NO 225, SEQ ID NO: 297, SEQ ID NO: 299, SEQ ID NO: 301 or orthologues or paralogues of any of the aforementioned SEQ ID NOs, preferably comprise a K/R ER configuration, more preferably an RER configuration, within the bHLH domain, typically within the basic region of the domain. The presence of this configuration is not a prerequisite to performing the methods of the invention, therefore some variation in the K/R ER configuration is acceptable. Arabidopsis bHLH polypeptides were grouped into twelve subfamilies according to structural similarities (see FIG. 4 of Heim et al., 2003). Members of group IX constitute bHLH polypeptides having an RER configuration. Furthermore, one member of Group VI comprises an RER configuration.

The polypeptides represented by any one of SEQ ID NO 213, SEQ ID NO 215, SEQ ID NO: 217, SEQ ID NO: 219, SEQ ID NO 225, SEQ ID NO: 297, SEQ ID NO: 299, SEQ ID NO: 301 or orthologues or paralogues of any of the aforementioned SEQ ID NOs, may also comprise (in addition to a bHLH domain and optionally a K/R ER 5-9-13 motif, preferably an RER motif) a domain designated PFB26111 (see Pfam database). The domain is also indicated in FIG. 18.

Typically, nucleic acids encoding bHLH transcription factors (as defined above) having a bHLH domain and having, in increasing order of preference, at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95% or more sequence identity to the PFB26111 domain (see FIG. 18) of any one of the polypeptides represented by any one of SEQ ID NO 213, SEQ ID NO 215, SEQ ID NO: 217, SEQ ID NO: 219, SEQ ID NO 225, SEQ ID NO: 297, SEQ ID NO: 299, or SEQ ID NO: 301 are useful in the methods of the invention.

Nucleic acids encoding the polypeptides represented by any one of SEQ ID NO 213, SEQ ID NO 215, SEQ ID NO: 217, SEQ ID NO: 219, SEQ ID NO 225, SEQ ID NO: 297, SEQ ID NO: 299, SEQ ID NO: 301, or orthologues or paralogues of any of the aforementioned SEQ ID NOs, need not be full-length nucleic acids, since performance of the methods of the invention does not rely on the use of full length nucleic acid sequences. Examples of nucleic acids suitable for use in performing the methods of the invention include but are not limited to those represented by any one of: SEQ ID NO: 212, SEQ ID NO: 214, SEQ ID NO: 216, SEQ ID NO: 218, SEQ ID NO: 220, SEQ ID NO: 222, SEQ ID NO: 224, SEQ ID NO: 226, SEQ ID NO: 228, SEQ ID NO: 296, SEQ ID NO: 298, and SEQ ID NO: 300. Nucleic acid variants may also be useful in practising the methods of the invention. Examples of such nucleic acid variants include portions of nucleic acids encoding a bHLH transcription factor as defined herein, splice variants of nucleic acids encoding a bHLH transcription factor as defined herein, allelic variants of nucleic acids encoding a bHLH transcription factor as defined herein and variants of nucleic acids encoding a bHLH transcription factor as defined herein that are obtained by gene shuffling. The terms portion, splice variant, allelic variant and gene shuffling will now be described.

A portion of a nucleic acids encoding a bHLH transcription factor as defined herein may be prepared, for example, by making one or more deletions to the nucleic acid. The portions may be used in isolated form or they may be fused to other coding (or non coding) sequences in order to, for example, produce a protein that combines several activities. When fused to other coding sequences, the resultant polypeptide produced upon translation may be bigger than that predicted for the bHLH transcription factor portion.

According to the present invention, there is provided a method for enhancing yield-related traits in plants, comprising introducing and expressing in a plant a portion of a nucleic acid encoding a bHLH transcription factor represented by any of SEQ ID NO 213, SEQ ID NO 215, SEQ ID NO: 217, SEQ ID NO: 219, SEQ ID NO 225, SEQ ID NO: 297, SEQ ID NO: 299, SEQ ID NO: 301, or a portion of a nucleic acid encoding orthologues, paralogues or homologues of any of the aforementioned SEQ ID NOs.

Portions useful in the methods of the invention, encode a polypeptide having a bHLH domain (as described above) and having substantially the same biological activity as the bHLH transcription factor represented by any of SEQ ID NO 213, SEQ ID NO 215, SEQ ID NO: 217, SEQ ID NO: 219, SEQ ID NO 225, SEQ ID NO: 297, SEQ ID NO: 299, SEQ ID NO: 301, or orthologues or paralogues of any of the aforementioned SEQ ID NOs. The portion is typically at least 150 consecutive nucleotides in length, preferably at least 300 consecutive nucleotides in length, more preferably at least 400 consecutive nucleotides in length and most preferably at least 500 consecutive nucleotides in length. Preferably, the portion is a portion of a nucleic acid as represented by any one of SEQ ID NO: 212, SEQ ID NO: 214, SEQ ID NO: 216, SEQ ID NO: 218, SEQ ID NO: 220, SEQ ID NO: 222, SEQ ID NO: 224, SEQ ID NO: 226, SEQ ID NO: 228, SEQ ID NO: 296, SEQ ID NO: 298, and SEQ ID NO: 300. Most preferably the portion is a portion of a nucleic acid as represented by SEQ ID NO: 212.

Another nucleic acid variant useful in the methods of the invention, is a nucleic acid capable of hybridising under reduced stringency conditions, preferably under stringent conditions, with a nucleic acid encoding a bHLH transcription factor as defined herein, or a with a portion as defined herein.

Hybridising sequences useful in the methods of the invention, encode a polypeptide having a bHLH domain (as described above) and having substantially the same biological activity as the bHLH transcription factor represented by any of SEQ ID NO 213, SEQ ID NO 215, SEQ ID NO: 217, SEQ ID NO: 219, SEQ ID NO 225, SEQ ID NO: 297, SEQ ID NO: 299, SEQ ID NO: 301 or having substantially the same biological activity as orthologues or paralogues of any of the aforementioned SEQ ID NOs. The hybridising sequence is typically at least 150 consecutive nucleotides in length, preferably at least 300 consecutive nucleotides in length, more preferably at least 400 consecutive nucleotides in length and most preferably at least 500 consecutive nucleotides in length. Preferably, the hybridising sequence is one that is capable of hybridising to any of the nucleic acids represented by SEQ ID NO: 212, SEQ ID NO: 214, SEQ ID NO: 216, SEQ ID NO: 218, SEQ ID NO: 220, SEQ ID NO: 222, SEQ ID NO: 224, SEQ ID NO: 226, SEQ ID NO: 228, SEQ ID NO: 296, SEQ ID NO: 298, and SEQ ID NO: 300 or to a portion of any of the aforementioned sequences, a portion being as defined above. Most preferably the hybridising sequence is capable of hybridising to a nucleic acid as represented by SEQ ID NO: 212, or to portions thereof.

According to the present invention, there is provided a method for enhancing yield-related traits in plants, comprising introducing and expressing in a plant a nucleic acid capable of hybridizing to a nucleic acid encoding a bHLH transcription factor represented by any of SEQ ID NO 213, SEQ ID NO 215, SEQ ID NO: 217, SEQ ID NO: 219, SEQ ID NO 225, SEQ ID NO: 297, SEQ ID NO: 299, SEQ ID NO: 301, or comprising introducing and expressing in a plant a nucleic acid capable of hybridising to a nucleic acid encoding an orthologue, paralogue or homologue of any of the aforementioned SEQ ID NOs.

Another nucleic acid variant useful in the methods of the invention is a splice variant encoding a bHLH transcription factor as defined hereinabove.

According to the present invention, there is provided a method for enhancing yield-related traits in plants, comprising introducing and expressing in a plant a splice variant of a nucleic acid encoding a bHLH transcription factor represented by any of SEQ ID NO 213, SEQ ID NO 215, SEQ ID NO: 217, SEQ ID NO: 219, SEQ ID NO 225, SEQ ID NO: 297, SEQ ID NO: 299, and SEQ ID NO: 301, or a splice variant of a nucleic acid encoding an orthologue, paralogue or homologue of any of the aforementioned SEQ ID NOs.

Preferred splice variants are splice variants of a nucleic acid encoding bHLH transcription factor represented by any of SEQ ID NO 213, SEQ ID NO 215, SEQ ID NO: 217, SEQ ID NO: 219, SEQ ID NO 225, SEQ ID NO: 297, SEQ ID NO: 299, and SEQ ID NO: 301, or splice variants encoding orthologues or paralogues of any of the aforementioned SEQ ID NOs. Further preferred are splice variants of nucleic acids represented by any one of SEQ ID NO: 212, SEQ ID NO: 214, SEQ ID NO: 216, SEQ ID NO: 218, SEQ ID NO: 220, SEQ ID NO: 222, SEQ ID NO: 224, SEQ ID NO: 226, SEQ ID NO: 228, SEQ ID NO: 296, SEQ ID NO: 298, and SEQ ID NO: 300. Most preferred is a splice variant of a nucleic acid as represented by SEQ ID NO: 212.

Another nucleic acid variant useful in performing the methods of the invention is an allelic variant of a nucleic acid encoding a bHLH transcription factor as defined hereinabove.

According to the present invention, there is provided a method for enhancing yield-related traits in plants, comprising introducing and expressing in a plant an allelic variant of a nucleic acid encoding a bHLH transcription factor represented by any of SEQ ID NO 213, SEQ ID NO 215, SEQ ID NO: 217, SEQ ID NO: 219, SEQ ID NO 225, SEQ ID NO: 297, SEQ ID NO: 299, and SEQ ID NO: 301, or comprising introducing and expressing in a plant an allelic variant of a nucleic acid encoding an orthologue, paralogue or homologue of any of the aforementioned SEQ ID NOs.

The allelic variant may be an allelic variant of a nucleic acid encoding a bHLH transcription factor represented by any of SEQ ID NO 213, SEQ ID NO 215, SEQ ID NO: 217, SEQ ID NO: 219, SEQ ID NO 225, SEQ ID NO: 297, SEQ ID NO: 299, and SEQ ID NO: 301, or an allelic variants of a nucleic acid encoding orthologues or paralogues of any of the aforementioned SEQ ID NOs. Further preferred are allelic variants of nucleic acids represented by any one of SEQ ID NO: 212, SEQ ID NO: 214, SEQ ID NO: 216, SEQ ID NO: 218, SEQ ID NO: 220, SEQ ID NO: 222, SEQ ID NO: 224, SEQ ID NO: 226 and SEQ ID NO: 228, SEQ ID NO: 296, SEQ ID NO: 298, SEQ ID NO: 300. Most preferred is an allelic variant of a nucleic acid as represented by SEQ ID NO: 212.

A further nucleic acid variant useful in the methods of the invention is a nucleic acid variant obtained by gene shuffling. Gene shuffling or directed evolution may also be used to generate variants of nucleic acids encoding bHLH transcription factors as defined above.

According to the present invention, there is provided a method for enhancing yield-related traits in plants, comprising introducing and expressing in a plant a variant of a nucleic acid encoding a bHLH transcription factor represented by any of SEQ ID NO 213, SEQ ID NO 215, SEQ ID NO: 217, SEQ ID NO: 219, SEQ ID NO 225, SEQ ID NO: 297, SEQ ID NO: 299, SEQ and ID NO: 301, or comprising introducing and expressing in a variant of a nucleic acid encoding an orthologue, paralogue or homologue of any of the aforementioned SEQ ID NOs, which nucleic acid is obtained by gene shuffling.

Furthermore, nucleic acid variants may also be obtained by site-directed mutagenesis. Several methods are available to achieve site-directed mutagenesis, the most common being PCR based methods (current protocols in molecular biology. Wiley Eds.).

Also useful in the methods of the invention are nucleic acids encoding homologues of any one of the amino acids represented by SEQ ID NO 213, SEQ ID NO 215, SEQ ID NO: 217, SEQ ID NO: 219, SEQ ID NO 225, SEQ ID NO: 297, SEQ ID NO: 299, SEQ ID NO: 301 or orthologues or paralogues of any of the aforementioned SEQ ID NOs.

Also useful in the methods of the invention are nucleic acids encoding derivatives of any one of the amino acids represented by SEQ ID NO 213, SEQ ID NO 215, SEQ ID NO: 217, SEQ ID NO: 219, SEQ ID NO 225, SEQ ID NO: 297, SEQ ID NO: 299, SEQ ID NO: 301 or orthologues or paralogues of any of the aforementioned SEQ ID NOs. Derivatives of SEQ ID NO: 215, SEQ ID NO: 217, SEQ ID NO: 219, SEQ ID NO: 221, SEQ ID NO: 223, SEQ ID NO: 225, SEQ ID NO: 227 and SEQ ID NO: 229, SEQ ID NO: 297, SEQ ID NO: 299, SEQ ID NO: 301 are further examples which may be suitable for use in the methods of the invention

Furthermore, bHLH transcription factors (at least in their native form) typically have DNA-binding activity and an activation domain. A person skilled in the art may easily determine the presence of an activation domain and DNA-binding activity using routine tools and techniques.

Nucleic acids encoding bHLH transcription factors may be derived from any natural or artificial source. The nucleic acid may be modified from its native form in composition and/or genomic environment through deliberate human manipulation. Preferably the bHLH transcription factor-encoding nucleic acid is from a plant, further preferably from a monocot, more preferably from the Poaceae family, most preferably the nucleic acid is from Oryza sativa.

Any reference herein to a bHLH transcription factor is therefore taken to mean a bHLH transcription factor as defined above. Any nucleic acid encoding such a bHLH transcription factor is suitable for use in performing the methods of the invention.

The present invention also encompasses plants or parts thereof (including plant cells) obtainable by the methods according to the present invention. The plants or parts thereof comprise a nucleic acid transgene encoding a bHLH transcription factor as defined above.

The invention also provides genetic constructs and vectors to facilitate introduction and/or expression of the nucleic acid sequences useful in the methods according to the invention, in a plant.

Therefore, there is provided a gene construct comprising:

-   -   (i) Any nucleic acid encoding a bHLH-type transcription factor         as defined hereinabove;     -   (ii) One or more control sequences operably liked to the nucleic         acid of (i).

Constructs useful in the methods according to the present invention may be constructed using recombinant DNA technology well known to persons skilled in the art. The gene constructs may be inserted into vectors, which may be commercially available, suitable for transforming into plants and suitable for expression of the gene of interest in the transformed cells. The invention therefore provides use of a gene construct as defined hereinabove in the methods of the invention.

Plants are transformed with a vector comprising the sequence of interest (i.e., a nucleic acid encoding a bHLH-type transcription factor). The skilled artisan is well aware of the genetic elements that must be present on the vector in order to successfully transform, select and propagate host cells containing the sequence of interest. The sequence of interest is operably linked to one or more control sequences (at least to a promoter).

Advantageously, any type of promoter, whether natural or synthetic, may be used to drive expression of the nucleic acid sequence. The promoter may be an inducible promoter, i.e. having induced or increased transcription initiation in response to a developmental, chemical, environmental or physical stimulus. The promoter may be a tissue-specific promoter, i.e. one that is capable of preferentially initiating transcription in certain tissues, such as the leaves, roots, seed tissue etc.

According to one preferred feature of the invention, the nucleic acid encoding a bHLH-type transcription factor is operably linked to a constitutive promoter. A constitutive promoter is transcriptionally active during most but not necessarily all phases of its growth and development and is substantially ubiquitously expressed. The constitutive promoter is preferably a GOS2 promoter, more preferably the constitutive promoter is a rice GOS2 promoter, further preferably the constitutive promoter is represented by a nucleic acid sequence substantially similar to SEQ ID NO: 230 or SEQ ID NO: 233, most preferably the constitutive promoter is as represented by SEQ ID NO: 233.

It should be clear that the applicability of the present invention is not restricted to the bHLH transcription factor-encoding nucleic acid represented by SEQ ID NO: 212, nor is the applicability of the invention restricted to expression of a such a bHLH transcription factor-encoding nucleic acid when driven by a GOS2 promoter. Examples of other constitutive promoters which may also be used perform the methods of the invention are shown in the definitions section.

Optionally, one or more terminator sequences (also a control sequence) may be used in the construct introduced into a plant. Additional regulatory elements may include transcriptional as well as translational enhancers. Those skilled in the art will be aware of terminator and enhancer sequences that may be suitable for use in performing the invention. Such sequences would be known or may readily be obtained by a person skilled in the art.

The genetic constructs of the invention may further include an origin of replication sequence that is required for maintenance and/or replication in a specific cell type. One example is when a genetic construct is required to be maintained in a bacterial cell as an episomal genetic element (e.g. plasmid or cosmid molecule). Preferred origins of replication include, but are not limited to, the f1-ori and colE1. Other control sequences (besides promoter, enhancer, silencer, intron sequences, 3′UTR and/or 5′UTR regions) may be protein and/or RNA stabilizing elements. The genetic construct may optionally comprise a selectable marker gene.

The invention also provides a method for the production of transgenic plants having enhanced yield-related traits relative to control plants, comprising introduction and expression in a plant of any nucleic acid encoding a bHLH-type transcription factor polypeptide as defined hereinabove.

More specifically, the present invention provides a method for the production of transgenic plants having enhanced yield-related traits, which method comprises:

-   -   (i) introducing and expressing a nucleic acid encoding a         bHLH-type transcription factor (as defined herein) in a plant         cell; and     -   (ii) cultivating the plant cell under conditions promoting plant         growth and development.

The nucleic acid may be introduced directly into a plant cell or into the plant itself (including introduction into a tissue, organ or any other part of a plant). According to a preferred feature of the present invention, the nucleic acid is preferably introduced into a plant by transformation.

Generally after transformation, plant cells or cell groupings are selected for the presence of one or more markers which are encoded by plant-expressible genes co-transferred with the gene of interest, following which the transformed material is regenerated into a whole plant.

Following DNA transfer and regeneration, putatively transformed plants may be evaluated, for instance using Southern analysis, for the presence of the gene of interest, copy number and/or genomic organisation. Alternatively or additionally, expression levels of the newly introduced DNA may be monitored using Northern and/or Western analysis, or quantitative PCR, all techniques being well known to persons having ordinary skill in the art.

The generated transformed plants may be propagated by a variety of means, such as by clonal propagation or classical breeding techniques. For example, a first generation (or T1) transformed plant may be selfed to give homozygous second generation (or T2) transformants, and the T2 plants further propagated through classical breeding techniques.

The generated transformed organisms may take a variety of forms. For example, they may be chimeras of transformed cells and non-transformed cells; clonal transformants (e.g., all cells transformed to contain the expression cassette); grafts of transformed and untransformed tissues (e.g., in plants, a transformed rootstock grafted to an untransformed scion).

The present invention clearly extends to any plant cell or plant produced by any of the methods described herein, and to all plant parts and propagules thereof. The present invention extends further to encompass the progeny of a primary transformed or transfected cell, tissue, organ or whole plant that has been produced by any of the aforementioned methods, the only requirement being that progeny exhibit the same genotypic and/or phenotypic characteristic(s) as those produced by the parent in the methods according to the invention.

The invention also includes host cells containing an isolated nucleic acid encoding a bHLH transcription factor as defined hereinabove. Preferred host cells according to the invention are plant cells.

The invention also extends to harvestable parts of a plant such as, but not limited to seeds, leaves, fruits, flowers, stems, rhizomes, tubers and bulbs. The invention furthermore relates to products derived, preferably directly derived, from a harvestable part of such a plant, such as dry pellets or powders, oil, fat and fatty acids, starch or proteins.

According to a preferred feature of the invention, the modulated expression is increased expression.

As mentioned above, a preferred method for modulating (preferably, increasing) expression of a nucleic acid encoding a bHLH transcription factor is by introducing and expressing in a plant a nucleic acid encoding a bHLH transcription factor; however the effects of performing the method, i.e. enhancing yield-related traits may also be achieved using other well known techniques. A description of some of these techniques will now follow.

One such technique is T-DNA activation tagging. The resulting transgenic plants show dominant phenotypes due to modified expression of genes close to the introduced promoter. The effects of the invention may also be reproduced using the technique of TILLING (Targeted Induced Local Lesions In Genomes). The effects of the invention may also be reproduced using homologous recombination.

Reference herein to the term enhanced yield-related traits is taken to mean an increase in biomass (weight) of one or more parts of a plant, which may include aboveground (harvestable) parts and/or (harvestable) parts below ground.

In particular, such harvestable parts are seeds, and performance of the methods of the invention results in plants having increased seed yield relative to the seed yield of control plants.

Taking corn as an example, a yield increase may be manifested as one or more of the following: increase in the number of plants established per hectare or acre, an increase in the number of ears per plant, an increase in the number of rows, number of kernels per row, kernel weight, thousand kernel weight, ear length/diameter, increase in the seed filling rate (which is the number of filled seeds divided by the total number of seeds and multiplied by 100), among others. Taking rice as an example, a yield increase may manifest itself as an increase in one or more of the following: number of plants per hectare or acre, number of panicles per plant, number of spikelets per panicle, number of flowers (florets) per panicle (which is expressed as a ratio of the number of filled seeds over the number of primary panicles), increase in the seed filling rate (which is the number of filled seeds divided by the total number of seeds and multiplied by 100), increase in thousand kernel weight, among others.

Since the transgenic plants according to the present invention have increased yield, it is likely that these plants exhibit an increased growth rate (during at least part of their life cycle), relative to the growth rate of corresponding wild type plants at a corresponding stage in their life cycle. The increased growth rate may be specific to one or more parts of a plant (including seeds), or may be throughout substantially the whole plant. A plant having an increased growth rate may even exhibit early flowering. The increase in growth rate may take place at one or more stages in the life cycle of a plant or during substantially the whole plant life cycle. Increased growth rate during the early stages in the life cycle of a plant may reflect enhanced vigour (increased seedling vigor at emergence). The increase in growth rate may alter the harvest cycle of a plant allowing plants to be sown later and/or harvested sooner than would otherwise be possible. If the growth rate is sufficiently increased, it may allow for the further sowing of seeds of the same plant species (for example sowing and harvesting of rice plants followed by sowing and harvesting of further rice plants all within one conventional growing period). Similarly, if the growth rate is sufficiently increased, it may allow for the further sowing of seeds of different plants species (for example the sowing and harvesting of corn plants followed by, for example, the sowing and optional harvesting of soy bean, potato or any other suitable plant). Harvesting additional times from the same rootstock in the case of some crop plants may also be possible. Altering the harvest cycle of a plant may lead to an increase in annual biomass production per acre (due to an increase in the number of times (say in a year) that any particular plant may be grown and harvested). An increase in growth rate may also allow for the cultivation of transgenic plants in a wider geographical area than their wild-type counterparts, since the territorial limitations for growing a crop are often determined by adverse environmental conditions either at the time of planting (early season) or at the time of harvesting (late season). Such adverse conditions may be avoided if the harvest cycle is shortened. The growth rate may be determined by deriving various parameters from growth curves, such parameters may be: T-Mid (the time taken for plants to reach 50% of their maximal size) and T-90 (time taken for plants to reach 90% of their maximal size), amongst others.

An increase in yield and/or growth rate occurs whether the plant is under non-stress conditions or whether the plant is exposed to various stresses compared to control plants. Plants typically respond to exposure to stress by growing more slowly. In conditions of severe stress, the plant may even stop growing altogether. Mild stress on the other hand is defined herein as being any stress to which a plant is exposed which does not result in the plant ceasing to grow altogether without the capacity to resume growth. Mild stress in the sense of the invention leads to a reduction in the growth of the stressed plants of less than 40%, 35% or 30%, preferably less than 25%, 20% or 15%, more preferably less than 14%, 13%, 12%, 11% or 10% or less in comparison to the control plant under non-stress conditions. Due to advances in agricultural practices (irrigation, fertilization, pesticide treatments) severe stresses are not often encountered in cultivated crop plants. As a consequence, the compromised growth induced by mild stress is often an undesirable feature for agriculture. Mild stresses are the everyday biotic and/or abiotic (environmental) stresses to which a plant is exposed. Abiotic stresses may be due to drought or excess water, anaerobic stress, salt stress, chemical toxicity, oxidative stress and hot, cold or freezing temperatures. The abiotic stress may be an osmotic stress caused by a water stress (particularly due to drought), salt stress, oxidative stress or an ionic stress. Biotic stresses are typically those stresses caused by pathogens, such as bacteria, viruses, fungi and insects.

In particular, the methods of the present invention may be performed under non-stress conditions or under conditions of mild drought to give plants having increased yield relative to control plants. As reported in Wang et al. (Planta (2003) 218: 1-14), abiotic stress leads to a series of morphological, physiological, biochemical and molecular changes that adversely affect plant growth and productivity. Drought, salinity, extreme temperatures and oxidative stress are known to be interconnected and may induce growth and cellular damage through similar mechanisms. Rabbani et al. (Plant Physiol (2003) 133: 1755-1767) describes a particularly high degree of “cross talk” between drought stress and high-salinity stress. For example, drought and/or salinisation are manifested primarily as osmotic stress, resulting in the disruption of homeostasis and ion distribution in the cell. Oxidative stress, which frequently accompanies high or low temperature, salinity or drought stress, may cause denaturing of functional and structural proteins. As a consequence, these diverse environmental stresses often activate similar cell signaling pathways and cellular responses, such as the production of stress proteins, up-regulation of anti-oxidants, accumulation of compatible solutes and growth arrest. The term “non-stress” conditions as used herein are those environmental conditions that allow optimal growth of plants. Persons skilled in the art are aware of normal soil conditions and climatic conditions for a given location.

Performance of the methods of the invention gives plants grown under non-stress conditions or under mild drought conditions increased yield relative to control plants grown under comparable conditions. Therefore, according to the present invention, there is provided a method for increasing yield in plants grown under non-stress conditions or under mild drought conditions, which method comprises increasing expression in a plant of a nucleic acid encoding a bHLH transcription factor.

Performance of the methods of the invention gives plants grown under conditions of nutrient deficiency, particularly under conditions of nitrogen deficiency, increased yield relative to control plants grown under comparable conditions. Therefore, according to the present invention, there is provided a method for increasing yield in plants grown under conditions of nutrient deficiency, which method comprises increasing expression in a plant of a nucleic acid encoding a MADS15 polypeptide. Nutrient deficiency may result from a lack or excess of nutrients such as nitrogen, phosphates and other phosphorous-containing compounds, potassium, calcium, cadmium, magnesium, manganese, iron and boron, amongst others.

According to a preferred feature of the present invention, performance of the methods of the invention gives plants having an increased growth rate relative to control plants, particularly during the early stages of plant development (typically three weeks post germination in the case of rice and maize, but this will vary from species to species) leading to early vigour. Therefore, according to the present invention, there is provided a method for increasing the growth rate of plants, which method comprises modulating, preferably increasing, expression in a plant of a nucleic acid encoding a bHLH transcription factor. The present invention therefore also provides a method for obtaining plants having early vigour relative to control plants, which method comprises modulating, preferably increasing, expression in a plant of a nucleic acid encoding a bHLH transcription factor.

Early vigour may also result from or be manifested as increased plant fitness relative to control plants due to, for example, the plants being better adapted to their environment (i.e. being more able to cope with various abiotic or biotic stress factors). Plants having early vigour also show better establishment of the crop (with the crop growing in uniform manner, i.e. with the majority of plants reaching the various stages of development at substantially the same time), and show better growth and often better yield. Early vigour may be determined by measuring various factors, such as seedling growth rate, thousand kernel weight, percentage germination, percentage emergence, seedling height, root length and shoot biomass and many more.

The methods of the invention are advantageously applicable to any plant.

Plants that are particularly useful in the methods of the invention include all plants which belong to the superfamily Viridiplantae, in particular monocotyledonous and dicotyledonous plants including fodder or forage legumes, ornamental plants, food crops, trees or shrubs. According to a preferred embodiment of the present invention, the plant is a crop plant. Examples of crop plants include soybean, sunflower, canola, alfalfa, rapeseed, cotton, tomato, potato and tobacco. Further preferably, the plant is a monocotyledonous plant. Examples of monocotyledonous plants include sugarcane. More preferably the plant is a cereal. Examples of cereals include rice, maize, wheat, barley, millet, rye, triticale, sorghum and oats. Plants in which early vigour is a particularly desirably trait include rice, maize, wheat, sunflower, sorghum.

The present invention also encompasses use of nucleic acids encoding bHLH transcription factors and use of bHLH transcription factor polypeptides in enhancing yield-related traits.

Nucleic acids encoding bHLH transcription factor polypeptides, or bHLH transcription factors themselves, may find use in breeding programmes in which a DNA marker is identified which may be genetically linked to a bHLH transcription factor-encoding gene. The nucleic acids/genes, or the bHLH transcription factors themselves may be used to define a molecular marker. This DNA or protein marker may then be used in breeding programmes to select plants having increased yield as defined hereinabove in the methods of the invention.

Allelic variants of a bHLH transcription factor-encoding acid/gene may also find use in marker-assisted breeding programmes. Such breeding programmes sometimes require introduction of allelic variation by mutagenic treatment of the plants, using for example EMS mutagenesis; alternatively, the programme may start with a collection of allelic variants of so called “natural” origin caused unintentionally. Identification of allelic variants then takes place, for example, by PCR. This is followed by a step for selection of superior allelic variants of the sequence in question and which give increased yield. Selection is typically carried out by monitoring growth performance of plants containing different allelic variants of the sequence in question. Growth performance may be monitored in a greenhouse or in the field. Further optional steps include crossing plants in which the superior allelic variant was identified with another plant. This could be used, for example, to make a combination of interesting phenotypic features.

A nucleic acid encoding a bHLH transcription factor may also be used as probes for genetically and physically mapping the genes that they are a part of, and as markers for traits linked to those genes. Such information may be useful in plant breeding in order to develop lines with desired phenotypes. Such use of bHLH transcription factor encoding nucleic acids requires only a nucleic acid sequence of at least 15 nucleotides in length. The bHLH transcription factor encoding nucleic acids may be used as restriction fragment length polymorphism (RFLP) markers. Southern blots (Sambrook J, Fritsch E F and Maniatis T (1989) Molecular Cloning, A Laboratory Manual) of restriction-digested plant genomic DNA may be probed with the bHLH transcription factor encoding nucleic acids. The resulting banding patterns may then be subjected to genetic analyses using computer programs such as MapMaker (Lander et al. (1987) Genomics 1: 174-181) in order to construct a genetic map. In addition, the nucleic acids may be used to probe Southern blots containing restriction endonuclease-treated genomic DNAs of a set of individuals representing parent and progeny of a defined genetic cross. Segregation of the DNA polymorphisms is noted and used to calculate the position of the bHLH transcription factor encoding nucleic acid in the genetic map previously obtained using this population (Botstein et al. (1980) Am. J. Hum. Genet. 32:314-331).

The production and use of plant gene-derived probes for use in genetic mapping is described in Bernatzky and Tanksley (1986) Plant Mol. Biol. Reporter 4: 37-41. Numerous publications describe genetic mapping of specific cDNA clones using the methodology outlined above or variations thereof. For example, F2 intercross populations, backcross populations, randomly mated populations, near isogenic lines, and other sets of individuals may be used for mapping. Such methodologies are well known to those skilled in the art.

The nucleic acid probes may also be used for physical mapping (i.e., placement of sequences on physical maps; see Hoheisel et al. In: Non-mammalian Genomic Analysis: A Practical Guide, Academic press 1996, pp. 319-346, and references cited therein).

In another embodiment, the nucleic acid probes may be used in direct fluorescence in situ hybridisation (FISH) mapping (Trask (1991) Trends Genet. 7:149-154). Although current methods of FISH mapping favor use of large clones (several kb to several hundred kb; see Laan et al. (1995) Genome Res. 5:13-20), improvements in sensitivity may allow performance of FISH mapping using shorter probes.

A variety of nucleic acid amplification-based methods for genetic and physical mapping may be carried out using the nucleic acids. Examples include allele-specific amplification (Kazazian (1989) J. Lab. Clin. Med. 11:95-96), polymorphism of PCR-amplified fragments (CAPS; Sheffield et al. (1993) Genomics 16:325-332), allele-specific ligation (Landegren et al. (1988) Science 241:1077-1080), nucleotide extension reactions (Sokolov (1990) Nucleic Acid Res. 18:3671), Radiation Hybrid Mapping (Walter et al. (1997) Nat. Genet. 7:22-28) and Happy Mapping (Dear and Cook (1989) Nucleic Acid Res. 17:6795-6807). For these methods, the sequence of a nucleic acid is used to design and produce primer pairs for use in the amplification reaction or in primer extension reactions. The design of such primers is well known to those skilled in the art. In methods employing PCR-based genetic mapping, it may be necessary to identify DNA sequence differences between the parents of the mapping cross in the region corresponding to the instant nucleic acid sequence. This, however, is generally not necessary for mapping methods.

The methods according to the present invention result in plants having enhnaced yield-related traits, as described hereinbefore. These traits may also be combined with other economically advantageous traits, such as further yield-enhancing traits, tolerance to other abiotic and biotic stresses, traits modifying various architectural features and/or biochemical and/or physiological features.

Detailed Description of SPL15

Surprisingly, it has now been found that increasing expression in a plant of a nucleic acid encoding an SPL15 transcription factor polypeptide gives plants having enhanced yield related traits, particularly increased yield, relative to control plants. Therefore, the invention provides a method for enhancing yield related traits in particular for increasing yield in plants relative to control plants, comprising increasing expression in a plant of a nucleic acid encoding an SPL15 transcription factor polypeptide.

A preferred method for increasing expression of a nucleic acid encoding a SPL15 transcription factor polypeptide is by introducing and expressing in a plant a nucleic acid encoding a SPL15 transcription factor polypeptide.

The term “SPL15 transcription factor polypeptide” as defined herein refers to a polypeptide comprising from N-terminal to C-terminal: (i) Motif 1 as represented by SEQ ID NO: 276; and (ii) in increasing order of preference at least 65%, 70%, 75%, 80%, 85%, 90%, 95% or 98% sequence identity to the SPL DBD represented by SEQ ID NO: 277; and (iii) Motif 2 as represented by SEQ ID NO: 278.

The most conserved amino acids within Motif 1 are XLXFGXXXYFX, and within Motif 2 DSXXALSLLSX (where X is a specified subset of amino acids differing for each position, as presented in SEQ ID NO: 276 and SEQ ID NO: 277). Within Motif 1 and Motif 2, are allowed one or more conservative change at any position, and/or one, two or three non-conservative change(s) at any position.

Additionally, the SPL15 transcription factor polypeptide may comprise any one or both of the following: (a) a G/S rich stretch preceding the SPL DBD; and (b) the W(S/T)L tripeptide at the C-terminal end of the polypeptide.

An example of an SPL15 transcription polypeptide as defined hereinabove comprising from N-terminal to C-terminal: (i) Motif 1 as represented by SEQ ID NO: 276; and (ii) in increasing order of preference at least 65%, 70%, 75%, 80%, 85%, 90%, 95% or 98% sequence identity to the SPL DBD represented by SEQ ID NO: 277; and (iii) Motif 2 as represented by SEQ ID NO: 278; and additionally comprising: (a) a G/S rich stretch preceding the SPL DBD; and (b) the W(S/T)L tripeptide at the C-terminal end of the polypeptide, is represented as in SEQ ID NO: 235. Further such examples are represented by any one of SEQ ID NO: 237, SEQ ID NO: 239, SEQ ID NO: 241, SEQ ID NO: 243, SEQ ID NO: 245, SEQ ID NO: 247, SEQ ID NO: 249, SEQ ID NO: 251, SEQ ID NO: 253, SEQ ID NO: 255, SEQ ID NO: 257, SEQ ID NO: 259, SEQ ID NO: 261, SEQ ID NO: 263, SEQ ID NO: 283, SEQ ID NO: 285, SEQ ID NO: 287 or orthologues or paralogues of any of the aforementioned SEQ ID NOs. The invention is illustrated by transforming plants with the Arabidopsis thaliana sequence represented by SEQ ID NO: 234, encoding the polypeptide of SEQ ID NO: 235. SEQ ID NO: 237 from Arabidopsis thaliana (encoded by SEQ ID NO: 236) is a paralogue of the polypeptide of SEQ ID NO: 235. SEQ ID NO: 239 (encoded by SEQ ID NO: 238, from Aquilegia formosa×Aquilegia pubescens), SEQ ID NO: 241 (encoded by SEQ ID NO: 240, from Gossypium hirsutum), SEQ ID NO: 243 (encoded by SEQ ID NO: 242, from Ipomoea nil), SEQ ID NO: 245 (encoded by SEQ ID NO: 244, from Lactuca sativa), SEQ ID NO: 247 (encoded by SEQ ID NO: 246, from Malus domestica), SEQ ID NO: 249 (encoded by SEQ ID NO: 248, from Medicago truncatula), SEQ ID NO: 251 (encoded by SEQ ID NO: 250, from Nicotiana bentamiana), SEQ ID NO: 253 (encoded by SEQ ID NO: 252, from Oryza sativa), SEQ ID NO: 255 (encoded by SEQ ID NO: 254, from Oryza sativa), SEQ ID NO: 257 (encoded by SEQ ID NO: 256, from Solanum tuberosum SEQ ID NO: 259 (encoded by SEQ ID NO: 258, from Vitis vinifera), SEQ ID NO: 261 (encoded by SEQ ID NO: 260, from Zea mays), SEQ ID NO: 263 (encoded by SEQ ID NO: 262, Zea mays), SEQ ID NO: 283 (encoded by SEQ ID NO: 282, Brassica rapa), SEQ ID NO: 285 (encoded by SEQ ID NO: 284, Glycine max), and SEQ ID NO: 287 (encoded by SEQ ID NO: 286, Populus tremuloides) are orthologues of the polypeptide of SEQ ID NO: 235.

Orthologues and paralogues may easily be found by performing a so-called reciprocal blast search. This may be done by a first BLAST involving BLASTing a query sequence (for example, SEQ ID NO: 234 or SEQ ID NO: 235) against any sequence database, such as the publicly available NCBI database. BLASTN or TBLASTX (using standard default values) may be used when starting from a nucleotide sequence and BLASTP or TBLASTN (using standard default values) may be used when starting from a polypeptide sequence. The BLAST results may optionally be filtered. The full-length sequences of either the filtered results or non-filtered results are then BLASTed back (second BLAST) against sequences from the organism from which the query sequence is derived (where the query sequence is SEQ ID NO: 234 or SEQ ID NO: 235, the second BLAST would therefore be against Arabidopsis sequences). The results of the first and second BLASTs are then compared. A paralogue is identified if a high-ranking hit from the first BLAST is from the same species as from which the query sequence is derived, a BLAST back then ideally results in the query sequence as highest hit (besides itself); an orthologue is identified if a high-ranking hit in the first BLAST is not from the same species as from which the query sequence is derived and preferably results upon BLAST back in the query sequence amongst the highest hits. High-ranking hits are those having a low E-value. The lower the E-value, the more significant the score (or in other words the lower the chance that the hit was found by chance). Computation of the E-value is well known in the art. In addition to E-values, comparisons are also scored by percentage identity. Percentage identity refers to the number of identical nucleotides (or amino acids) between the two compared nucleic acid (or polypeptide) sequences over a particular length. An example detailing the identification of orthologues and paralogues is given in Example 41. In the case of large families, ClustalW may be used, followed by a neighbour joining tree, to help visualize clustering of related genes and to identify orthologues and paralogues. In FIG. 22, the SPL15 transcription factor polypeptide paralogues and orthologues cluster together.

The polypeptides represented by any one of SEQ ID NO: 237, SEQ ID NO: 239, SEQ ID NO: 241, SEQ ID NO: 243, SEQ ID NO: 245, SEQ ID NO: 247, SEQ ID NO: 249, SEQ ID NO: 251, SEQ ID NO: 253, SEQ ID NO: 255, SEQ ID NO: 257, SEQ ID NO: 259, SEQ ID NO: 261, SEQ ID NO: 263, SEQ ID NO: 283, SEQ ID NO: 285, SEQ ID NO: 287, or orthologues or paralogues of any of the aforementioned SEQ ID NOs, all comprise an SPL DBD having, in increasing order of preference, at least 65%, 70%, 75%, 80%, 85%, 90%, 95% or 98% sequence identity to the SPL15 DBD represented by SEQ ID NO: 277.

SPL DBDs are well known in the art and may readily be identified by persons skilled in the art. A SPL DBD may be identified using methods for the alignment of sequences for comparison. Methods for the alignment of sequences for comparison include GAP, BESTFIT, BLAST, FASTA and TFASTA. GAP uses the algorithm of Needleman and Wunsch ((1970) J Mol Biol 48: 443-453) to find the alignment of two complete sequences that maximizes the number of matches and minimizes the number of gaps. The BLAST algorithm (Altschul et al. (1990) J Mol Biol 215: 403-10) calculates percent sequence identity and performs a statistical analysis of the similarity between the two sequences. The software for performing BLAST analysis is publicly available through the National Centre for Biotechnology Information. Homologues may readily be identified using, for example, the ClustalW multiple sequence alignment algorithm (version 1.83) available at GenomeNet service at the Kyoto University Bioinformatics Center, with the default pairwise alignment parameters, and a scoring method in percentage. Minor manual editing may be performed to optimise alignment between conserved motifs, as would be apparent to a person skilled in the art. The alignment shown in FIGS. 23 and 24 highlight the SPL DBD in SPL15 transcription factor polypeptides. Preferably, SPL15 transcription factor polypeptides useful in the methods of the invention comprise an SPL DBD having, in increasing order of preference, at least 65%, 70%, 75%, 80%, 85%, 90%, 95% or 98% sequence identity to the SPL DBD represented by SEQ ID NO: 277.

In some instances, default parameters may be adjusted to modify the stringency of the search. For example using BLAST, the statistical significance threshold (called “expect” value) for reporting matches against database sequences may be increased to show less stringent matches. In this way, short nearly exact matches may be identified. Motif 1 as represented by SEQ ID NO: 276 and Motif 2 as represented by SEQ ID NO: 278 both comprised in the SPL15 transcription factor polypeptides useful in the methods of the invention may be identified this way (FIG. 24). Within Motif 1 and Motif 2, are allowed one or more conservative change at any position, and/or one, two or three non-conservative change(s) at any position. The W(S/T)L tripeptide at the C-terminal end of the polypeptide may likewise be identified (FIG. 24).

Special databases also exisit for the identification of domains. The SPL DBD in a SPL15 transcription factor polypeptide may be identified using, for example, SMART (Schultz et al. (1998) Proc. Natl. Acad. Sci. USA 95, 5857-5864; Letunic et al. (2002) Nucleic Acids Res 30, 242-244; hosted by the EMBL at Heidelberg, Germany), InterPro (Mulder et al., (2003) Nucl. Acids. Res. 31, 315-318; hosted by the European Bioinformatics Institute (EBI) in the United Kingdom), Prosite (Bucher and Bairoch (1994), A generalized profile syntax for biomolecular sequences motifs and its function in automatic sequence interpretation. (In) ISMB-94; Proceedings 2nd International Conference on Intelligent Systems for Molecular Biology. Altman R., Brutlag D., Karp P., Lathrop R., Searls D., Eds., pp 53-61, AAAIPress, Menlo Park; Hulo et al., Nucl. Acids. Res. 32: D134-D137, (2004), The ExPASy proteomics server is provided as a service to the scientific community (hosted by the Swiss Institute of Bioinformatics (SIB) in Switzerland) or Pfam (Bateman et al., Nucleic Acids Research 30(1): 276-280 (2002), hosted by the Sanger Institute in the United Kingdom). The SPL DBD in the InterPro database is designated IPR004333, PF03110 in the Pfam database and PS51141 in the PROSITE database.

Furthermore, the presence of G/S rich stretch preceding the SPL DBD may also readily be identified (FIG. 24). Primary amino acid composition (in %) to determine if a polypeptide domain is rich in specific amino acids may be calculated using software programs from the ExPASy server, in particular the ProtParam tool (Gasteiger E et al. (2003) ExPASy: the proteomics server for in-depth protein knowledge and analysis. Nucleic Acids Res 31:3784-3788). The composition of the protein of interest may then be compared to the average amino acid composition (in %) in the Swiss-Prot Protein Sequence data bank. Within this databank, the average Gly (G) and Ser (E) content are both of 6.9% (adding up to 13.8%). As an example, the G/S rich stretch preceding the SPL DBD of SEQ ID NO: 235 contains 14.5% of G and 25.5% of S (adding up to 40%). As defined herein, a G/S rich stretch has a combined G and S content (in % terms) above that found in the average amino acid composition (in % terms) of the proteins in the Swiss-Prot Protein Sequence. Both G and S belong to the category of very small amino acids.

The nucleic acid encoding the polypeptides represented by any one of SEQ ID NO: 235, SEQ ID NO: 237, SEQ ID NO: 239, SEQ ID NO: 241, SEQ ID NO: 243, SEQ ID NO: 245, SEQ ID NO: 247, SEQ ID NO: 249, SEQ ID NO: 251, SEQ ID NO: 253, SEQ ID NO: 255, SEQ ID NO: 257, SEQ ID NO: 259, SEQ ID NO: 261, SEQ ID NO: 263, SEQ ID NO: 283, SEQ ID NO: 285, SEQ ID NO: 287, or orthologues or paralogues of any of the aforementioned SEQ ID NOs, need not be full-length nucleic acids, since performance of the methods of the invention does not rely on the use of full length nucleic acid sequences. Furthermore, examples of nucleic acids suitable for use in performing the methods of the invention include but are not limited to those represented by any one of: SEQ ID NO: 234, SEQ ID NO: 236, SEQ ID NO: 238, SEQ ID NO: 240, SEQ ID NO: 242, SEQ ID NO: 244, SEQ ID NO: 246, SEQ ID NO: 248, SEQ ID NO: 250, SEQ ID NO: 252, SEQ ID NO: 254, SEQ ID NO: 256, SEQ ID NO: 258, SEQ ID NO: 260, SEQ ID NO: 262, SEQ ID NO: 282, SEQ ID NO: 284 and SEQ ID NO: 286. Nucleic acid variants may also be useful in practising the methods of the invention. Examples of such variants include portions of nucleic acids, splice variants, allelic variants either naturally occurring or obtained by DNA manipulation.

A portion may be prepared, for example, by making one or more deletions to a nucleic acid encoding a SPL15 transcription factor polypeptide as defined hereinabove. The portions may be used in isolated form or they may be fused to other coding (or non coding) sequences in order to, for example, produce a protein that combines several activities. When fused to other coding sequences, the resultant polypeptide produced upon translation may be bigger than that predicted for the SPL15 transcription factor portion. Portions useful in the methods of the invention, encode an SPL15 transcription factor polypeptide (as described above) and having substantially the same biological activity as the SPL15 transcription factor polypeptide represented by any of SEQ ID NO: 235, SEQ ID NO: 237, SEQ ID NO: 239, SEQ ID NO: 241, SEQ ID NO: 243, SEQ ID NO: 245, SEQ ID NO: 247, SEQ ID NO: 249, SEQ ID NO: 251, SEQ ID NO: 253, SEQ ID NO: 255, SEQ ID NO: 257, SEQ ID NO: 259, SEQ ID NO: 261, SEQ ID NO: 263, SEQ ID NO: 283, SEQ ID NO: 285, SEQ ID NO: 287, or orthologues or paralogues of any of the aforementioned SEQ ID NOs. Examples of portions may include the nucleotides encoding Motif 1 as represented by SEQ ID NO: 276, in increasing order of preference at least 65%, 70%, 75%, 80%, 85%, 90%, 95% or 98% sequence identity to the SPL DBD represented by SEQ ID NO: 277, and Motif 2 as represented by SEQ ID NO: 278. Portions may additionally include nucleotides encoding the G/S rich stretch or the W(S/T)L tripeptide (but not necessarily the nucleotides encoding the amino acid sequences between any of these). The portion is typically at least 250 nucleotides in length, preferably at least 500 nucleotides in length, more preferably at least 750 nucleotides in length and most preferably at least 1000 nucleotides in length. Preferably, the portion is a portion of a nucleic acid as represented by any one of SEQ ID NO: 234, SEQ ID NO: 236, SEQ ID NO: 238, SEQ ID NO: 240, SEQ ID NO: 242, SEQ ID NO: 244, SEQ ID NO: 246, SEQ ID NO: 248, SEQ ID NO: 250, SEQ ID NO: 252, SEQ ID NO: 254, SEQ ID NO: 256, SEQ ID NO: 258, SEQ ID NO: 260, SEQ ID NO: 262, SEQ ID NO: 282, SEQ ID NO: 284 and SEQ ID NO: 286. Most preferably the portion is a portion of a nucleic acid as represented by SEQ ID NO: 234.

Another nucleic acid variant useful in the methods of the invention, is a nucleic acid capable of hybridising under reduced stringency conditions, preferably under stringent conditions, with a nucleic acid encoding a SPL15 transcription factor polypeptide as defined hereinabove, or a with a portion as defined hereinabove.

Hybridising sequences useful in the methods of the invention, encode a polypeptide comprising from N-terminal to C-terminal: (i) Motif 1 as represented by SEQ ID NO: 276; and (ii) in increasing order of preference at least 65%, 70%, 75%, 80%, 85%, 90%, 95% or 98% sequence identity to the SPL DBD represented by SEQ ID NO: 277; and (iii) Motif 2 as represented by SEQ ID NO: 278, and having substantially the same biological activity as the SPL15 transcription factor polypeptides represented by SEQ ID NO: 235, SEQ ID NO: 237, SEQ ID NO: 239, SEQ ID NO: 241, SEQ ID NO: 243, SEQ ID NO: 245, SEQ ID NO: 247, SEQ ID NO: 249, SEQ ID NO: 251, SEQ ID NO: 253, SEQ ID NO: 255, SEQ ID NO: 257, SEQ ID NO: 259, SEQ ID NO: 261, SEQ ID NO: 263, SEQ ID NO: 283, SEQ ID NO: 285, SEQ ID NO: 287, or orthologues or paralogues of any of the aforementioned SEQ ID NOs. The hybridising sequence is typically at least 250 nucleotides in length, preferably at least 500 nucleotides in length, more preferably at least 750 nucleotides in length and most preferably at least 1000 nucleotides in length. Preferably, the hybridising sequence is one that is capable of hybridising to any of the nucleic acids represented by SEQ ID NO: 234, SEQ ID NO: 236, SEQ ID NO: 238, SEQ ID NO: 240, SEQ ID NO: 242, SEQ ID NO: 244, SEQ ID NO: 246, SEQ ID NO: 248, SEQ ID NO: 250, SEQ ID NO: 252, SEQ ID NO: 254, SEQ ID NO: 256, SEQ ID NO: 258, SEQ ID NO: 260, SEQ ID NO: 262, SEQ ID NO: 282, SEQ ID NO: 284 and SEQ ID NO: 286, or to a portion of any of the aforementioned sequences, a portion being as defined above. Most preferably the hybridising sequence is capable of hybridising to SEQ ID NO: 234, or to portions thereof.

Another nucleic acid variant useful in the methods of the invention is a splice variant encoding a SPL15 transcription factor polypeptide as defined hereinabove.

Preferred splice variants are splice variants of a nucleic acid encoding SPL15 transcription factor polypeptide represented by any of SEQ ID NO: 235, SEQ ID NO: 237, SEQ ID NO: 239, SEQ ID NO: 241, SEQ ID NO: 243, SEQ ID NO: 245, SEQ ID NO: 247, SEQ ID NO: 249, SEQ ID NO: 251, SEQ ID NO: 253, SEQ ID NO: 255, SEQ ID NO: 257, SEQ ID NO: 259, SEQ ID NO: 261, SEQ ID NO: 263, SEQ ID NO: 283, SEQ ID NO: 285, or SEQ ID NO: 287, or splice variants encoding orthologues or paralogues of any of the aforementioned SEQ ID NO: 234, SEQ ID NO: 236, SEQ ID NO: 238, SEQ ID NO: 240, SEQ ID NO: 242, SEQ ID NO: 244, SEQ ID NO: 246, SEQ ID NO: 248, SEQ ID NO: 250, SEQ ID NO: 252, SEQ ID NO: 254, SEQ ID NO: 256, SEQ ID NO: 258, SEQ ID NO: 260, SEQ ID NO: 262, SEQ ID NO: 282, SEQ ID NO: 284 and SEQ ID NO: 286. Most preferred is a splice variant of a nucleic acid as represented by SEQ ID NO: 234.

Another nucleic acid variant useful in performing the methods of the invention is an allelic variant of a nucleic acid encoding a SPL15 transcription factor polypeptide as defined hereinabove.

The allelic variant may be an allelic variant of a nucleic acid encoding a SPL15 transcription factor polypeptide represented by any of SEQ ID NO: 235, SEQ ID NO: 237, SEQ ID NO: 239, SEQ ID NO: 241, SEQ ID NO: 243, SEQ ID NO: 245, SEQ ID NO: 247, SEQ ID NO: 249, SEQ ID NO: 251, SEQ ID NO: 253, SEQ ID NO: 255, SEQ ID NO: 257, SEQ ID NO: 259, SEQ ID NO: 261, SEQ ID NO: 263, SEQ ID NO: 283, SEQ ID NO: 285, or SEQ ID NO: 287, or an allelic variant of a nucleic acid encoding orthologues or paralogues of any of the aforementioned SEQ ID NOs. Further preferred are allelic variants of nucleic acids represented by any one of SEQ ID NO: 234, SEQ ID NO: 236, SEQ ID NO: 238, SEQ ID NO: 240, SEQ ID NO: 242, SEQ ID NO: 244, SEQ ID NO: 246, SEQ ID NO: 248, SEQ ID NO: 250, SEQ ID NO: 252, SEQ ID NO: 254, SEQ ID NO: 256, SEQ ID NO: 258, SEQ ID NO: 260, SEQ ID NO: 262, SEQ ID NO: 282, SEQ ID NO: 284 and SEQ ID NO: 286. Most preferred is an allelic variant of a nucleic acid as represented by SEQ ID NO: 234.

A further nucleic acid variant useful in the methods of the invention is a nucleic acid variant obtained by gene shuffling. Gene shuffling or directed evolution may also be used to generate variants of nucleic acids encoding SPL15 transcription factor polypeptides as defined above.

Furthermore, nucleic acid variants may also be obtained by site-directed mutagenesis. Several methods are available to achieve site-directed mutagenesis, the most common being PCR based methods (Current Protocols in Molecular Biology. Wiley (Eds)).

Also useful in the methods of the invention are nucleic acids encoding homologues of any one of the amino acids represented by SEQ ID NO: 235, SEQ ID NO: 237, SEQ ID NO: 239, SEQ ID NO: 241, SEQ ID NO: 243, SEQ ID NO: 245, SEQ ID NO: 247, SEQ ID NO: 249, SEQ ID NO: 251, SEQ ID NO: 253, SEQ ID NO: 255, SEQ ID NO: 257, SEQ ID NO: 259, SEQ ID NO: 261, SEQ ID NO: 263, SEQ ID NO: 283, SEQ ID NO: 285, SEQ ID NO: 287, or orthologues or paralogues of any of the aforementioned SEQ ID NOs.

Also useful in the methods of the invention are nucleic acids encoding derivatives of any one of the amino acids represented by SEQ ID NO: 235, SEQ ID NO: 237, SEQ ID NO: 239, SEQ ID NO: 241, SEQ ID NO: 243, SEQ ID NO: 245, SEQ ID NO: 247, SEQ ID NO: 249, SEQ ID NO: 251, SEQ ID NO: 253, SEQ ID NO: 255, SEQ ID NO: 257, SEQ ID NO: 259, SEQ ID NO: 261 SEQ ID NO: 263, SEQ ID NO: 283, SEQ ID NO: 285, SEQ ID NO: 287, or orthologues or paralogues of any of the aforementioned SEQ ID NOs. “Derivatives” include peptides, oligopeptides, polypeptides which may, compared to the amino acid sequence of the naturally-occurring form of the protein, such as the one presented in SEQ ID NO: 235, comprise substitutions of amino acids with non-naturally occurring amino acid residues, or additions of non-naturally occurring amino acid residues.

Furthermore, SPL15 transcription factor polypeptides (at least in their native form) typically have DNA-binding activity and an activation domain. A person skilled in the art may easily determine the presence of an activation domain and DNA-binding activity using routine tools and techniques.

Nucleic acids encoding SPL15 transcription factor polypeptides may be derived from any natural or artificial source. The nucleic acid may be modified from its native form in composition and/or genomic environment through deliberate human manipulation. Preferably the SPL15 transcription factor polypeptide-encoding nucleic acid is from a plant, further preferably from a dicot, more preferably from the Brassicacea family, most preferably the nucleic acid is from Arabidopsis thaliana.

Any reference herein to a SPL15 transcription factor polypeptide is therefore taken to mean a SPL15 transcription factor peptide as defined above. Any nucleic acid encoding such a SPL15 transcription factor polypeptide is suitable for use in performing the methods of the invention.

The invention also provides genetic constructs and vectors to facilitate introduction and/or expression of the nucleic acid sequences useful in the methods according to the invention, in a plant.

Therefore, there is provided a gene construct comprising:

-   -   (i) A nucleic acid encoding a SPL15 transcription factor         polypeptide as defined hereinabove;     -   (ii) One or more control sequences operably liked to the nucleic         acid of (i).

Constructs useful in the methods according to the present invention may be constructed using recombinant DNA technology well known to persons skilled in the art. The gene constructs may be inserted into vectors, which may be commercially available, suitable for transforming into plants and suitable for expression of the gene of interest in the transformed cells. The invention therefore provides use of a gene construct as defined hereinabove in the methods of the invention.

Plants are transformed with a vector comprising the sequence of interest (i.e., a nucleic acid encoding a SPL15 transcription factor polypeptide). The skilled artisan is well aware of the genetic elements that must be present on the vector in order to successfully transform, select and propagate host cells containing the sequence of interest. The sequence of interest is operably linked to one or more control sequences (at least to a promoter).

Advantageously, any type of promoter, whether natural or synthetic, may be used to drive expression of the nucleic acid sequence. The promoter may be an inducible promoter, i.e. having induced or increased transcription initiation in response to a developmental, chemical, environmental or physical stimulus. The promoter may be a tissue-specific promoter, i.e. one that is capable of preferentially initiating transcription in certain tissues, such as the leaves, roots, seed tissue etc.

According to the invention, the nucleic acid encoding a SPL15 transcription factor polypeptide is operably linked to a constitutive promoter. The constitutive promoter is preferably a HMGB (high mobility group B) promoter, more preferably the constitutive promoter is a rice HMGB promoter, further preferably the constitutive promoter is represented by a nucleic acid sequence substantially similar to SEQ ID NO: 279, most preferably the constitutive promoter is as represented by SEQ ID NO: 279 or SEQ ID NO: 294.

It should be clear that the applicability of the present invention is not restricted to the nucleic acid encoding an SPL15 transcription factor polypeptide as represented by SEQ ID NO: 234, nor is the applicability of the invention restricted to expression of a such nucleic acid encoding an SPL15 transcription factor polypeptide when driven by a HMGB promoter. Examples of other constitutive promoters which may also be used perform the methods of the invention are shown in the definitions section.

Additional regulatory elements for increasing expression of nucleic acids or genes, or gene products, may include transcriptional as well as translational enhancers. Those skilled in the art will be aware of terminator and enhancer sequences that may be suitable for use in performing the invention. Other control sequences (besides promoter, enhancer, silencer, intron sequences, 3′UTR and/or 5′UTR regions) may be protein and/or RNA stabilizing elements. Such sequences would be known or may readily be obtained by a person skilled in the art. Optionally, one or more terminator sequences (also a control sequence) may be used in the construct introduced into a plant.

An intron sequence may also be added to the 5′ untranslated region (UTR) or the coding sequence of the partial coding sequence to increase the amount of the mature message that accumulates in the cytosol.

The genetic constructs of the invention may further include an origin of replication sequence that is required for maintenance and/or replication in a specific cell type. One example is when a genetic construct is required to be maintained in a bacterial cell as an episomal genetic element (e.g. plasmid or cosmid molecule). Preferred origins of replication include, but are not limited to, the f1-ori and colE1.

The genetic construct may optionally comprise a selectable marker gene.

The invention also provides a method for the production of transgenic plants having increased yield relative to control plants, comprising introduction and expression in a plant of a nucleic acid encoding a SPL15 transcription factor polypeptide as defined hereinabove.

More specifically, the present invention provides a method for the production of transgenic plants having increased yield relative to control plants, which method comprises:

-   -   (i) introducing and expressing a nucleic acid encoding a SPL15         transcription factor polypeptide in a plant cell; and     -   (ii) cultivating the plant cell under conditions promoting plant         growth and development.

The nucleic acid may be introduced directly into a plant cell or into the plant itself (including introduction into a tissue, organ or any other part of a plant). According to a preferred feature of the present invention, the nucleic acid is preferably introduced into a plant by transformation.

Generally after transformation, plant cells or cell groupings are selected for the presence of one or more markers which are encoded by plant-expressible genes co-transferred with the gene of interest, following which the transformed material is regenerated into a whole plant.

Following DNA transfer and regeneration, putatively transformed plants may be evaluated, for instance using Southern analysis, for the presence of the gene of interest, copy number and/or genomic organisation. Alternatively or additionally, expression levels of the newly introduced DNA may be monitored using Northern and/or Western analysis, or quantitative PCR, all techniques being well known to persons having ordinary skill in the art.

The generated transformed plants may be propagated by a variety of means, such as by clonal propagation or classical breeding techniques. For example, a first generation (or T1) transformed plant may be selfed to give homozygous second generation (or T2) transformants, and the T2 plants further propagated through classical breeding techniques.

The generated transformed organisms may take a variety of forms. For example, they may be chimeras of transformed cells and non-transformed cells; clonal transformants (e.g., all cells transformed to contain the expression cassette); grafts of transformed and untransformed tissues (e.g., in plants, a transformed rootstock grafted to an untransformed scion).

The present invention clearly extends to any plant cell or plant produced by any of the methods described herein, and to all plant parts and propagules thereof. The present invention extends further to encompass the progeny of a primary transformed or transfected cell, tissue, organ or whole plant that has been produced by any of the aforementioned methods, the only requirement being that progeny exhibit the same genotypic and/or phenotypic characteristic(s) as those produced by the parent in the methods according to the invention.

The invention also includes host cells containing an isolated nucleic acid encoding a SPL15 transcription factor polypeptide as defined hereinabove. Preferred host cells according to the invention are plant cells.

The invention also extends to harvestable parts of a plant such as, but not limited to seeds, leaves, fruits, flowers, stems, rhizomes, tubers and bulbs. The invention furthermore relates to products derived, preferably directly derived, from a harvestable part of such a plant, such as dry pellets or powders, oil, fat and fatty acids, starch or proteins.

As mentioned above, a preferred method for increasing expression of a nucleic acid encoding a SPL15 transcription factor polypeptide is by introducing and expressing in a plant a nucleic acid encoding a SPL15 transcription factor polypeptide; however the effects of performing the method, i.e. increasing yield, may also be achieved using other well known techniques. A description of some of these techniques will now follow.

One such technique is T-DNA activation tagging. The resulting transgenic plants show dominant phenotypes due to modified expression of genes close to the introduced promoter.

The effects of the invention may also be reproduced using the technique of TILLING (Targeted Induced Local Lesions In Genomes).

The effects of the invention may also be reproduced using homologous recombination.

“Increased yield” as defined herein is taken to mean an increase in biomass (weight) of one or more parts of a plant, which may include aboveground (harvestable) parts and/or (harvestable) parts below ground.

In particular, such harvestable parts include vegetative biomass and/or seeds, and performance of the methods of the invention results in plants having increased yield (in vegetative biomass and/or seed) relative to the yield of control plants.

Taking corn as an example, a yield increase may be manifested as one or more of the following: increase in the number of plants per hectare or acre, an increase in the number of ears per plant, an increase in the number of rows, number of kernels per row, kernel weight, thousand kernel weight, ear length/diameter, increase in the seed filling rate (which is the number of filled seeds divided by the total number of seeds and multiplied by 100), among others. Taking rice as an example, a yield increase may manifest itself as an increase in one or more of the following: number of plants per hectare or acre, number of panicles per plant, number of spikelets per panicle, number of flowers (florets) per panicle (which is expressed as a ratio of the number of filled seeds over the number of primary panicles), increase in the seed filling rate (which is the number of filled seeds divided by the total number of seeds and multiplied by 100), increase in thousand kernel weight, among others.

Since the transgenic plants according to the present invention have increased yield, it is likely that these plants exhibit an increased growth rate (during at least part of their life cycle), relative to the growth rate of corresponding wild type plants at a corresponding stage in their life cycle. The increased growth rate may be specific to one or more parts of a plant (including seeds), or may be throughout substantially the whole plant. A plant having an increased growth rate may even exhibit early flowering. The increase in growth rate may alter the harvest cycle of a plant allowing plants to be sown later and/or harvested sooner than would otherwise be possible. If the growth rate is sufficiently increased, it may allow for the further sowing of seeds of the same plant species (for example sowing and harvesting of rice plants followed by sowing and harvesting of further rice plants all within one conventional growing period). Similarly, if the growth rate is sufficiently increased, it may allow for the further sowing of seeds of different plants species (for example the sowing and harvesting of corn plants followed by, for example, the sowing and optional harvesting of soy bean, potato or any other suitable plant). Harvesting additional times from the same rootstock in the case of some crop plants may also be possible. Altering the harvest cycle of a plant may lead to an increase in annual biomass production per acre (due to an increase in the number of times (say in a year) that any particular plant may be grown and harvested). An increase in growth rate may also allow for the cultivation of transgenic plants in a wider geographical area than their wild-type counterparts, since the territorial limitations for growing a crop are often determined by adverse environmental conditions either at the time of planting (early season) or at the time of harvesting (late season). Such adverse conditions may be avoided if the harvest cycle is shortened. The growth rate may be determined by deriving various parameters from growth curves, such parameters may be: T-Mid (the time taken for plants to reach 50% of their maximal size) and T-90 (time taken for plants to reach 90% of their maximal size), amongst others.

According to a preferred feature of the present invention, performance of the methods of the invention gives plants having an increased growth rate relative to control plants. Therefore, according to the present invention, there is provided a method for increasing the growth rate of plants, which method comprises increasing expression in a plant of a nucleic acid encoding a SPL15 transcription factor polypeptide

An increase in yield and/or growth rate occurs whether the plant is under non-stress conditions or whether the plant is exposed to various stresses compared to control plants. Plants typically respond to exposure to stress by growing more slowly. In conditions of severe stress, the plant may even stop growing altogether. Mild stress on the other hand is defined herein as being any stress to which a plant is exposed which does not result in the plant ceasing to grow altogether without the capacity to resume growth. Mild stress in the sense of the invention leads to a reduction in the growth of the stressed plants of less than 40%, 35% or 30%, preferably less than 25%, 20% or 15%, more preferably less than 14%, 13%, 12%, 11% or 10% or less in comparison to the control plant under non-stress conditions. Due to advances in agricultural practices (irrigation, fertilization, pesticide treatments) severe stresses are not often encountered in cultivated crop plants. As a consequence, the compromised growth induced by mild stress is often an undesirable feature for agriculture. Mild stresses are the everyday biotic and/or abiotic (environmental) stresses to which a plant is exposed. Abiotic stresses may be due to drought or excess water, anaerobic stress, salt stress, chemical toxicity, oxidative stress and hot, cold or freezing temperatures. The abiotic stress may be an osmotic stress caused by a water stress (particularly due to drought), salt stress, oxidative stress or an ionic stress. Biotic stresses are typically those stresses caused by pathogens, such as bacteria, viruses, fungi and insects.

In particular, the methods of the present invention may be performed under non-stress conditions or under conditions of mild drought to give plants having increased yield relative to control plants. As reported in Wang et al. (Planta (2003) 218: 1-14), abiotic stress leads to a series of morphological, physiological, biochemical and molecular changes that adversely affect plant growth and productivity. Drought, salinity, extreme temperatures and oxidative stress are known to be interconnected and may induce growth and cellular damage through similar mechanisms. Rabbani et al. (Plant Physiol (2003) 133: 1755-1767) describes a particularly high degree of “cross talk” between drought stress and high-salinity stress. For example, drought and/or salinisation are manifested primarily as osmotic stress, resulting in the disruption of homeostasis and ion distribution in the cell. Oxidative stress, which frequently accompanies high or low temperature, salinity or drought stress, may cause denaturing of functional and structural proteins. As a consequence, these diverse environmental stresses often activate similar cell signaling pathways and cellular responses, such as the production of stress proteins, up-regulation of anti-oxidants, accumulation of compatible solutes and growth arrest. The term “non-stress” conditions as used herein are those environmental conditions that allow optimal growth of plants. Persons skilled in the art are aware of normal soil conditions and climatic conditions for a given location.

Performance of the methods of the invention gives plants grown under non-stress conditions or under mild drought conditions increased yield relative to control plants grown under comparable conditions. Therefore, according to the present invention, there is provided a method for increasing yield in plants grown under non-stress conditions or under mild drought conditions, which method comprises increasing expression in a plant of a nucleic acid encoding a MADS15 polypeptide.

Performance of the methods of the invention gives plants grown under conditions of nutrient deficiency, particularly under conditions of nitrogen deficiency, increased yield relative to control plants grown under comparable conditions. Therefore, according to the present invention, there is provided a method for increasing yield in plants grown under conditions of nutrient deficiency, which method comprises increasing expression in a plant of a nucleic acid encoding a MADS15 polypeptide. Nutrient deficiency may result from a lack or excess of nutrients such as nitrogen, phosphates and other phosphorous-containing compounds, potassium, calcium, cadmium, magnesium, manganese, iron and boron, amongst others.

The methods of the invention are advantageously applicable to any plant.

Plants that are particularly useful in the methods of the invention include all plants which belong to the superfamily Viridiplantae, in particular monocotyledonous and dicotyledonous plants including fodder or forage legumes, ornamental plants, food crops, trees or shrubs. According to a preferred embodiment of the present invention, the plant is a crop plant. Examples of crop plants include soybean, sunflower, canola, alfalfa, rapeseed, cotton, tomato, potato and tobacco. Further preferably, the plant is a monocotyledonous plant. Examples of monocotyledonous plants include sugarcane. More preferably the plant is a cereal. Examples of cereals include rice, maize, wheat, barley, millet, rye, triticale, sorghum and oats.

The present invention also encompasses plants obtainable by the methods according to the present invention. The present invention therefore provides plants, parts and cells from such plants obtainable by the methods according to the present invention, which plants or parts or cells comprise a nucleic acid transgene encoding a SPL15 transcription factor polypeptide as defined above.

The present invention also encompasses use of nucleic acids encoding SPL15 transcription factor polypeptides in increasing yield in a plant compared to yield in a control plant.

One such use relates to increasing yield of plants, yield being defined as defined herein above. Yield may in particular include one or more of the following: increased aboveground biomass, increased number of flowers per panicle, increased seed yield, increased total number of seeds, increased number of filled seeds, increased thousand kernel weight (TKW) and increased harvest index.

Nucleic acids encoding SPL15 transcription factor polypeptides may find use in breeding programmes in which a DNA marker is identified which may be genetically linked to a gene encoding SPL15 transcription factor polypeptide. Nucleic acids encoding SPL15 transcription factor polypeptides may be used to define a molecular marker. This marker may then be used in breeding programmes to select plants having increased seed yield. The nucleic acids encoding SPL15 transcription factor polypeptides may be, for example, a nucleic acid as represented by any one of SEQ ID NO: 234, SEQ ID NO: 236, SEQ ID NO: 238, SEQ ID NO: 240, SEQ ID NO: 242, SEQ ID NO: 244, SEQ ID NO: 246, SEQ ID NO: 248, SEQ ID NO: 250, SEQ ID NO: 252, SEQ ID NO: 254, SEQ ID NO: 256, SEQ ID NO: 258, SEQ ID NO: 260, SEQ ID NO: 262, SEQ ID NO: 282, SEQ ID NO: 284 and SEQ ID NO: 286.

Allelic variants of a nucleic acid encoding an SPL15 transcription factor polypeptide may also find use in marker-assisted breeding programmes. Such breeding programmes sometimes require introduction of allelic variation by mutagenic treatment of the plants, using for example EMS mutagenesis; alternatively, the programme may start with a collection of allelic variants of so called “natural” origin caused unintentionally. Identification of allelic variants then takes place, for example, by PCR. This is followed by a step for selection of superior allelic variants of the sequence in question and which give increased seed yield. Selection is typically carried out by monitoring growth performance of plants containing different allelic variants of the sequence in question, for example, different allelic variants of any one of SEQ ID NO: 234, SEQ ID NO: 236, SEQ ID NO: 238, SEQ ID NO: 240, SEQ ID NO: 242, SEQ ID NO: 244, SEQ ID NO: 246, SEQ ID NO: 248, SEQ ID NO: 250, SEQ ID NO: 252, SEQ ID NO: 254, SEQ ID NO: 256, SEQ ID NO: 258, SEQ ID NO: 260, SEQ ID NO: 262, SEQ ID NO: 282, SEQ ID NO: 284 and SEQ ID NO: 286. Growth performance may be monitored in a greenhouse or in the field. Further optional steps include crossing plants, in which the superior allelic variant was identified, with another plant. This could be used, for example, to make a combination of interesting phenotypic features.

Nucleic acids encoding SPL15 transcription factor polypeptides may also be used as probes for genetically and physically mapping the genes that they are a part of, and as markers for traits linked to those genes. Such information may be useful in plant breeding in order to develop lines with desired phenotypes. Such use of nucleic acids encoding SPL15 transcription factor polypeptides requires only a nucleic acid sequence of at least 15 nucleotides in length. The nucleic acids encoding SPL15 transcription factor polypeptides may be used as restriction fragment length polymorphism (RFLP) markers. Southern blots (Sambrook J, Fritsch E F and Maniatis T (1989) Molecular Cloning, A Laboratory Manual) of restriction-digested plant genomic DNA may be probed with a nucleic acid encoding SPL15 transcription factor polypeptide. The resulting banding patterns may then be subjected to genetic analyses using computer programs such as MapMaker (Lander et al. (1987) Genomics 1: 174-181) in order to construct a genetic map. In addition, the nucleic acid may be used to probe Southern blots containing restriction endonuclease-treated genomic DNAs of a set of individuals representing parent and progeny of a defined genetic cross. Segregation of the DNA polymorphisms is noted and used to calculate the position of the nucleic acid encoding SPL15 transcription factor polypeptide in the genetic map previously obtained using this population (Botstein et al. (1980) Am. J. Hum. Genet. 32: 314-331).

The production and use of plant gene-derived probes for use in genetic mapping is described in Bernatzky and Tanksley (GENETICS 112 (4): 887-898, 1986). Numerous publications describe genetic mapping of specific cDNA clones using the methodology outlined above or variations thereof. For example, F2 intercross populations, backcross populations, randomly mated populations, near isogenic lines (NIL), and other sets of individuals may be used for mapping. Such methodologies are well known to those skilled in the art.

The nucleic acid probes may also be used for physical mapping (i.e., placement of sequences on physical maps; see Hoheisel et al. In: Non-mammalian Genomic Analysis: A Practical Guide, Academic press 1996, pp. 319-346, and references cited therein).

In another embodiment, the nucleic acid probes may be used in direct fluorescence in situ hybridization (FISH) mapping (Trask (1991) Trends Genet. 7:149-154). Although current methods of FISH mapping favour use of large clones (several kb to several hundred kb; see Laan et al. (1995) Genome Res. 5:13-20), improvements in sensitivity may allow performance of FISH mapping using shorter probes.

A variety of nucleic acid amplification-based methods for genetic and physical mapping may be carried out using the nucleic acids. Examples include allele-specific amplification (Kazazian (1989) J. Lab. Clin. Med. 11:95-96), polymorphism of PCR-amplified fragments (CAPS; Sheffield et al. (1993) Genomics 16:325-332), allele-specific ligation (Landegren et al. (1988) Science 241:1077-1080), nucleotide extension reactions (Sokolov (1990) Nucleic Acid Res. 18:3671), Radiation Hybrid Mapping (Walter et al. (1997) Nat. Genet. 7:22-28) and Happy Mapping (Dear and Cook (1989) Nucleic Acid Res. 17:6795-6807). For these methods, the sequence of a nucleic acid is used to design and produce primer pairs for use in the amplification reaction or in primer extension reactions. The design of such primers is well known to those skilled in the art. In methods employing PCR-based genetic mapping, it may be necessary to identify DNA sequence differences between the parents of the mapping cross in the region corresponding to the instant nucleic acid sequence. This, however, is generally not necessary for mapping methods.

The methods according to the present invention result in plants having increased yield, as described hereinbefore. These traits may also be combined with other economically advantageous traits, such as further yield-increasing traits, tolerance to other abiotic and biotic stresses, traits modifying various architectural features and/or biochemical and/or physiological features.

DESCRIPTION OF FIGURES

The present invention will now be described with reference to the following figures in which:

FIG. 1 represents the schematic structure of the AtHAL3a polypeptide comprising from N-terminus to C-terminus (i) the substrate binding helix (single underlined), (ii) the insertion His motif (double underlined), (iii) the PXMNXXMW motif (dotted) and (iv) the substrate recognition clamp (wave underlined). The N-terminal and C-terminal ends of the HAL3 proteins are not very conserved.

FIG. 2 shows a binary vector pEXP::HAL3, for increased expression in Oryza sativa of an Arabidopsis thaliana HAL3 nucleic acid under the control of a beta expansin promoter.

FIG. 3 shows a multiple alignment of a number of HAL3 sequences from Arabidopsis thaliana AtHAL3b (At_NP_(—)973994), Sorghum bicolor (Sb), Arabidopsis thaliana AtHAL3a (Ath0218), Gossipium hirsutum (Cg), Hordeum vulgare (Hv), Oryza sativa (Os), Vitis vinifera (Vv), Glycine max (Gm), Solanum tuberosum (St), Zea mays (Zm), and Pinus sp (Pg).

FIG. 4 details examples of sequences useful in performing the methods according to the present invention: SEQ ID NO: 1 and SEQ ID NO: 2 represent the nucleic acid sequence and the protein sequence of AtHAl3a. SEQ ID NO: 3 and SEQ ID NO: 4 are the sequences of the forward and reverse primers used to isolate the AtHAL3 gene. SEQ ID NO: 5 is the sequence of the beta expansin promoter used in the methods of the present invention. SEQ ID NO: 9 to SEQ ID NO: 42 represent examples of full length or partial DNA/protein sequences, useful in the methods of the invention or for isolating corresponding full length sequences. In some cases, sequences were assembled from EST sequences, with lesser quality sequencing. As a consequence, a few nucleic acid substitutions may be expected.

FIG. 5 (A) shows the domain structure of the MADS15 protein, (B) represents the sequence of SEQ ID NO: 44 with the MADS domain in bold and the keratin domain in italics. Between the MADS domain and the keratin, the intervening domain is located while the C-domain is located C-terminally of the keratin domain.

FIG. 6 shows a multiple alignment of various MADS15 proteins. The asterisks indicate identical amino acids, the colons represent highly conservative substitutions, the dots represent less conserved substitutions.

FIG. 7 shows the binary vector for increased expression in Oryza sativa of an Oryza sativa MADS15 protein-encoding nucleic acid under the control of a GOS2 promoter.

FIG. 8 details examples of sequences useful in performing the methods according to the present invention.

FIG. 9 is a schematic representation of a full-length OsMADS15 polypeptide. The typical domains (M, MADS; I, intervening domain; K, keratin K-box region; C, variable C-terminal region) are indicated, the lines above and below the diagram show the regions of the protein involved in DNA binding, dimerisation and in multimerisation with interacting proteins.

FIG. 10 shows the binary vector pGOS::MADS15hp for MADS15 RNA silencing in Oryza sativa, using a hairpin construct under the control of a constitutive promoter (GOS2).

FIG. 11 details examples of sequences useful in performing the methods according to the present invention, or useful in isolating such sequences. Sequences may result from public EST assemblies, with lesser quality sequencing. As a consequence, a few nucleic acid substitutions may be expected. The start (ATG) and stop codons delimit the nucleic acid sequences when these encode full-length MADS15 polypeptides. However both 5′ and 3′ UTR may also be used for the performing the methods of the invention.

FIG. 12 shows the schematic classification of the AP2/ERF transcription factor polypeptides according to the domains present: the AP2 subfamily with two AP2 repeats and the ERF subfamily with only one AP2 repeat. The ERF subfamily is further subdivided into transcription factors comprising a B3 domain in addition to the AP2 repeat (called RAV), or not. The PLT transcription factor polypeptides belong to the AP2 subfamily with two AP2 repeats.

FIG. 13 represents a schematic presentation of the PLT transcription factor polypeptide structure. The AP2 domain comprises the two AP2 repeats (boxed) separated by a linker region. The approximate positions of the nuclear localisation signal (NLS), of motif 1 PK(V/L)(A/E)DFLG and of motif 2 (V/L)FX(M/V)WN(D/E) are marked as boxes.

FIG. 14 is an alignment of PLT transcription factor polypeptide sequences (from Table 4), compared to other AP2 domain transcription factor polypeptides (from Table 4 below). The nuclear localisation signal (NLS), motif 1 PK(V/L)(A/E)DFLG and motif 2 (V/L)FX(M/V)WN(D/E) are boxed. Identical residues are blackened, conservative residues are grayed.

TABLE 4 AP2 domain transcription factor polypeptides aligned against the PLT transcription factor polypeptides used to perform the methods of the invention. Name NCBI accession number Source Arath_ANT NM_119937 Arabidopsis thaliana Arath_BBM NM_121749.1 Arabidopsis thaliana Brana_BBM1 AF317904 Brassica napus Brana_BBM2 AF317905 Brassica napus Medtr_AP2 BBM AY899909 Medicago truncatula Nicta_ANT like AY461432 Nicotiana tabacum Orysa_AP2 XM_473084 Oryza sativa Pinth_ANTL1 AB101585 Pinus thunbergii Zeama_AP2 AY109146.1 Zea mays

FIG. 15 is a photograph of 40 seeds from a control plant (left) compared to 40 seeds from a transgenic plant with increased expression of a PLT transcription factor polypeptide.

FIG. 16 shows a binary vector pGOS2::PLT, for increased expression in Oryza sativa of an Oryza sativa PLT transcription factor nucleic acid under the control of a GOS2 promoter.

FIG. 17 details examples of sequences useful in performing the methods according to the present invention (SEQ ID NO: 175 to SEQ ID NO: 188). Partial sequences (SEQ ID NO: 189 and SEQ ID NO: 190) useful in isolating corresponding full length sequences are also presented.

FIG. 18 shows an alignment of bHLH transcription factors as defined hereinabove. The sequences were aligned using AlignX program from Vector NTI suite (InforMax, Bethesda, Md.). Multiple alignment was done with a gap opening penalty of 10 and a gap extension of 0.01. Minor manual editing was also carried out where necessary to better position some conserved regions. The bHLH domain is indicated within the solid box and the PFB26111 domain is indicated within the dashed box. Also indicated by the three upwardly pointing arrows is the 5-9-13 configuration (K/R ER). The single downwardly pointing arrow indicates the glutamic acid reside for recognition of the E-BOX.

FIG. 19 shows a matrix of similarity and identity between bHLH transcription factors from various species. Percentage identity is shown in bold. FIG. 19 a is a matrix over full length sequences and FIG. 19 b is a matrix over the bHLH domain only. More details are provided in Example 34.

FIG. 20 shows a binary vector pGOS2::bHLH, for increased expression in Oryza sativa of an Oryza sativa bHLH transcription factor-encoding nucleic acid under the control of a GOS2 promoter.

FIG. 21 details examples of sequences useful in performing the methods according to the present invention.

FIG. 22 Neighbour-joining tree output after a multiple sequence alignment of all Arabidopsis thaliana SPL transcription factor polypeptides and of SPL15 transcription factor polypeptide orthologues using CLUSTAL W (1.83) (at GenomeNet service at the Kyoto University Bioinformatics Center), and default values (Blosum 62 as weight matrix, gap open penalty of 10; gap extension penalty of 0.05). Arabidopsis thaliana SPL15 transcription factor polypeptide clusters with the other SPL15 transcription factor polypeptide orthologues and paralogues, as shown by the curly bracket.

FIG. 23 shows an alignment of the DNA-binding domain (DBD) of SPL15 transcription factor polypeptide orthologues and paralogs. The sequences were aligned using AlignX program from Vector NTI suite (InforMax, Bethesda, Md.). Multiple alignment was done with a gap opening penalty of 10 and a gap extension of 0.01. The conserved Cys and His residues involved in zinc ion binding are boxed. The bipartite nuclear localization signal (NLS) is underlined.

FIG. 24 is an alignment of SPL15 transcription factor polypeptide orthologues and paralogues. The sequences were aligned using AlignX program from Vector NTI suite (InforMax, Bethesda, Md.). Multiple alignment was done with a gap opening penalty of 10 and a gap extension of 0.01. Minor manual editing was also carried out where necessary to better position some conserved regions. The three main characterized domains, from N-terminal to C-terminal, are boxed and identified as Motif 1, the SPL DNA binding domain and Motif 2. Additionally, the G/S rich stretch preceding the SPL DBD is marked with Xs and the W(S/T)L tripeptide at the C-terminal end of the polypeptide also boxed.

FIG. 25 shows a binary vector pHMGB::SPL15, for increased expression in Oryza sativa of an Arabidopsis thaliana nucleic acid encoding an SPL15 transcription factor polypeptide under the control of an HMGB promoter.

FIG. 26 details examples of sequences useful in performing the methods according to the present invention.

EXAMPLES

The present invention will now be described with reference to the following examples, which are by way of illustration alone. The following examples are not intended to completely define or otherwise limit the scope of the invention.

DNA manipulation: unless otherwise stated, recombinant DNA techniques are performed according to standard protocols described in (Sambrook (2001) Molecular Cloning: a laboratory manual, 3rd Edition Cold Spring Harbor Laboratory Press, CSH, New York) or in Volumes 1 and 2 of Ausubel et al. (1994), Current Protocols in Molecular Biology, Current Protocols. Standard materials and methods for plant molecular work are described in Plant Molecular Biology Labfax (1993) by R.D.D. Croy, published by BIOS Scientific Publications Ltd (UK) and Blackwell Scientific Publications (UK).

Example Section A HAL3 Example 1 Identification of Sequences Related to the Nucleic Acid Sequence Used in the Methods of the Invention

Sequences (full length cDNA, ESTs or genomic) related to the nucleic acid sequence used in the methods of the present invention were identified amongst those maintained in the Entrez Nucleotides database at the National Center for Biotechnology Information (NCBI) using database sequence search tools, such as the Basic Local Alignment Tool (BLAST) (Altschul et al. (1990) J. Mol. Biol. 215:403-410; and Altschul et al. (1997) Nucleic Acids Res. 25:3389-3402). The program is used to find regions of local similarity between sequences by comparing nucleic acid or polypeptide sequences to sequence databases and by calculating the statistical significance of matches. For example, the polypeptide encoded by the nucleic acid of the present invention was used for the TBLASTN algorithm, with default settings and the filter to ignore low complexity sequences set off. The output of the analysis was viewed by pairwise comparison, and ranked according to the probability score (E-value), where the score reflect the probability that a particular alignment occurs by chance (the lower the E-value, the more significant the hit). In addition to E-values, comparisons were also scored by percentage identity. Percentage identity refers to the number of identical nucleotides (or amino acids) between the two compared nucleic acid (or polypeptide) sequences over a particular length. In some instances, the default parameters may be adjusted to modify the stringency of the search. For example the E-value may be increased to show less stringent matches. This way, short nearly exact matches may be identified.

Table A provides a list of nucleic acid sequences related to the nucleic acid sequence used in the methods of the present invention.

TABLE A Examples of HAL3 polypeptides: Nucleic acid Protein Plant Source SEQ ID NO: SEQ ID NO: Arabidopsis thaliana 9 10 Oryza sativa 11 12 Triticum aestivum 13 14 Zea mays 15 16 Picea abies 17 18 Brassica napus 19 20 Brassica oleracea 21 22 Nicotiana tabacum 23 24 Solanum tuberosum 25 26 Glycine max 27 28 Vitis vinifera 29 30 Hordeum vulgare 31 32 Gossypium hirsutum 33 34 Sorghum bicolor 35 36 Lycopersicon esculentum 37 38 Arabidopsis thaliana 39 40 Pinus sp. 41 42

In some instances, related sequences have tentatively been assembled and publicly disclosed by research institutions, such as The Institute for Genomic Research (TIGR). The Eukaryotic Gene Orthologs (EGO) database may be used to identify such related sequences, either by keyword search or by using the BLAST algorithm with the nucleic acid or polypeptide sequence of interest.

Example 2 Cloning of the Nucleic Acid Sequence Used in the Methods of the Invention

The nucleic acid sequence used in the methods of the invention was amplified by PCR using as template a custom-made Arabidopsis thaliana seedlings cDNA library (in pCMV Sport 6.0; Invitrogen, Paisley, UK). PCR was performed using Hifi Taq DNA polymerase in standard conditions, using 200 ng of template in a 50 μl PCR mix. The primers used were prm00957 (SEQ ID NO: 3; sense, start codon in bold:

5′ aaaaagcaggctcacaatggagaatgggaaaagagac 3′) and prm00958 (SEQ ID NO: 4; reverse, complementary,:

5′ agaaagctgggttggttttaactagttccaccg 3′), which include the AttB sites for Gateway recombination. The amplified PCR fragment was purified also using standard methods. The first step of the Gateway procedure, the BP reaction, was then performed, during which the PCR fragment recombines in vivo with the pDONR201 plasmid to produce, according to the Gateway terminology, an “entry clone”, pHAL3. Plasmid pDONR201 was purchased from Invitrogen, as part of the Gateway® technology.

Example 3 Expression Vector Construction

The entry clone pHAL3 was subsequently used in an LR reaction with pEXP, a destination vector used for Oryza sativa transformation. This vector contains as functional elements within the T-DNA borders: a plant selectable marker; a screenable marker expression cassette; and a Gateway cassette intended for LR in vivo recombination with the nucleic acid sequence of interest already cloned in the entry clone. A rice beta expansin promoter (SEQ ID NO: 5) for shoot-specific expression was located upstream of this Gateway cassette.

After the LR recombination step, the resulting expression vector pEXP::HAL3 (FIG. 2) was transformed into Agrobacterium strain LBA4044 and subsequently to Oryza sativa plants.

Example 4 Crop Transformation

The transformed Agrobacterium containing the expression vectors were used independently to transform Oryza sativa plants. Mature dry seeds of the rice japonica cultivar Nipponbare were dehusked. Sterilization was carried out by incubating for one minute in 70% ethanol, followed by 30 minutes in 0.2% HgCl₂, followed by a 6 times 15 minutes wash with sterile distilled water. The sterile seeds were then germinated on a medium containing 2,4-D (callus induction medium). After incubation in the dark for four weeks, embryogenic, scutellum-derived calli were excised and propagated on the same medium. After two weeks, the calli were multiplied or propagated by subculture on the same medium for another 2 weeks. Embryogenic callus pieces were sub-cultured on fresh medium 3 days before co-cultivation (to boost cell division activity).

Agrobacterium strain LBA4404 containing the expression vector was used for co-cultivation. Agrobacterium was inoculated on AB medium with the appropriate antibiotics and cultured for 3 days at 28° C. The bacteria were then collected and suspended in liquid co-cultivation medium to a density (OD₆₀₀) of about 1. The suspension was then transferred to a Petri dish and the calli immersed in the suspension for 15 minutes. The callus tissues were then blotted dry on a filter paper and transferred to solidified, co-cultivation medium and incubated for 3 days in the dark at 25° C. Co-cultivated calli were grown on 2,4-D-containing medium for 4 weeks in the dark at 28° C. in the presence of a selection agent. During this period, rapidly growing resistant callus islands developed. After transfer of this material to a regeneration medium and incubation in the light, the embryogenic potential was released and shoots developed in the next four to five weeks. Shoots were excised from the calli and incubated for 2 to 3 weeks on an auxin-containing medium from which they were transferred to soil. Hardened shoots were grown under high humidity and short days in a greenhouse.

The primary transformants were transferred from a tissue culture chamber to a greenhouse. After a quantitative PCR analysis to verify copy number of the T-DNA insert, only single copy transgenic plants that exhibit tolerance to the selection agent were kept for harvest of T1 seed. Seeds were then harvested three to five months after transplanting. The method yielded single locus transformants at a rate of over 50% (Aldemita and Hodges1996, Chan et al. 1993, Hiei et al. 1994).

Corn Transformation

Transformation of maize (Zea mays) is performed with a modification of the method described by Ishida et al. (1996) Nature Biotech 14(6): 745-50. Transformation is genotype-dependent in corn and only specific genotypes are amenable to transformation and regeneration. The inbred line A188 (University of Minnesota) or hybrids with A188 as a parent are good sources of donor material for transformation, but other genotypes can be used successfully as well. Ears are harvested from corn plant approximately 11 days after pollination (DAP) when the length of the immature embryo is about 1 to 1.2 mm. Immature embryos are cocultivated with Agrobacterium tumefaciens containing the expression vector, and transgenic plants are recovered through organogenesis. Excised embryos are grown on callus induction medium, then maize regeneration medium, containing the selection agent (for example imidazolinone but various selection markers can be used). The Petri plates are incubated in the light at 25° C. for 2-3 weeks, or until shoots develop. The green shoots are transferred from each embryo to maize rooting medium and incubated at 25° C. for 2-3 weeks, until roots develop. The rooted shoots are transplanted to soil in the greenhouse. T1 seeds are produced from plants that exhibit tolerance to the selection agent and that contain a single copy of the T-DNA insert.

Wheat Transformation

Transformation of wheat is performed with the method described by Ishida et al. (1996) Nature Biotech 14(6): 745-50. The cultivar Bobwhite (available from CIMMYT, Mexico) is commonly used in transformation. Immature embryos are co-cultivated with Agrobacterium tumefaciens containing the expression vector, and transgenic plants are recovered through organogenesis. After incubation with Agrobacterium, the embryos are grown in vitro on callus induction medium, then regeneration medium, containing the selection agent (for example imidazolinone but various selection markers can be used). The Petri plates are incubated in the light at 25° C. for 2-3 weeks, or until shoots develop. The green shoots are transferred from each embryo to rooting medium and incubated at 25° C. for 2-3 weeks, until roots develop. The rooted shoots are transplanted to soil in the greenhouse. T1 seeds are produced from plants that exhibit tolerance to the selection agent and that contain a single copy of the T-DNA insert.

Soybean Transformation

Soybean is transformed according to a modification of the method described in the Texas A&M U.S. Pat. No. 5,164,310. Several commercial soybean varieties are amenable to transformation by this method. The cultivar Jack (available from the Illinois Seed foundation) is commonly used for transformation. Soybean seeds are sterilised for in vitro sowing. The hypocotyl, the radicle and one cotyledon are excised from seven-day old young seedlings. The epicotyl and the remaining cotyledon are further grown to develop axillary nodes. These axillary nodes are excised and incubated with Agrobacterium tumefaciens containing the expression vector. After the cocultivation treatment, the explants are washed and transferred to selection media. Regenerated shoots are excised and placed on a shoot elongation medium. Shoots no longer than 1 cm are placed on rooting medium until roots develop. The rooted shoots are transplanted to soil in the greenhouse. T1 seeds are produced from plants that exhibit tolerance to the selection agent and that contain a single copy of the T-DNA insert.

Rapeseed/Canola Transformation

Cotyledonary petioles and hypocotyls of 5-6 day old young seedling are used as explants for tissue culture and transformed according to Babic et al. (1998, Plant Cell Rep 17: 183-188). The commercial cultivar Westar (Agriculture Canada) is the standard variety used for transformation, but other varieties can also be used. Canola seeds are surface-sterilized for in vitro sowing. The cotyledon petiole explants with the cotyledon attached are excised from the in vitro seedlings, and inoculated with Agrobacterium (containing the expression vector) by dipping the cut end of the petiole explant into the bacterial suspension. The explants are then cultured for 2 days on MSBAP-3 medium containing 3 mg/l BAP, 3% sucrose, 0.7% Phytagar at 23° C., 16 hr light. After two days of co-cultivation with Agrobacterium, the petiole explants are transferred to MSBAP-3 medium containing 3 mg/l BAP, cefotaxime, carbenicillin, or timentin (300 mg/l) for 7 days, and then cultured on MSBAP-3 medium with cefotaxime, carbenicillin, or timentin and selection agent until shoot regeneration. When the shoots are 5-10 mm in length, they are cut and transferred to shoot elongation medium (MSBAP-0.5, containing 0.5 mg/l BAP). Shoots of about 2 cm in length are transferred to the rooting medium (MS0) for root induction. The rooted shoots are transplanted to soil in the greenhouse. T1 seeds are produced from plants that exhibit tolerance to the selection agent and that contain a single copy of the T-DNA insert.

Alfalfa Transformation

A regenerating clone of alfalfa (Medicago sativa) is transformed using the method of (McKersie et al., 1999 Plant Physiol 119: 839-847). Regeneration and transformation of alfalfa is genotype dependent and therefore a regenerating plant is required. Methods to obtain regenerating plants have been described. For example, these can be selected from the cultivar Rangelander (Agriculture Canada) or any other commercial alfalfa variety as described by Brown D C W and A Atanassov (1985. Plant Cell Tissue Organ Culture 4: 111-112). Alternatively, the RA3 variety (University of Wisconsin) has been selected for use in tissue culture (Walker et al., 1978 Am J Bot 65:654-659). Petiole explants are cocultivated with an overnight culture of Agrobacterium tumefaciens C58C1 pMP90 (McKersie et al., 1999 Plant Physiol 119: 839-847) or LBA4404 containing the expression vector. The explants are cocultivated for 3 d in the dark on SH induction medium containing 288 mg/L Pro, 53 mg/L thioproline, 4.35 g/L K₂SO₄, and 100 μm acetosyringinone. The explants are washed in half-strength Murashige-Skoog medium (Murashige and Skoog, 1962) and plated on the same SH induction medium without acetosyringinone but with a suitable selection agent and suitable antibiotic to inhibit Agrobacterium growth. After several weeks, somatic embryos are transferred to BOi2Y development medium containing no growth regulators, no antibiotics, and 50 g/L sucrose. Somatic embryos are subsequently germinated on half-strength Murashige-Skoog medium. Rooted seedlings were transplanted into pots and grown in a greenhouse. T1 seeds are produced from plants that exhibit tolerance to the selection agent and that contain a single copy of the T-DNA insert.

Example 5 Evaluation Procedure 5.1 Evaluation Setup

Approximately 30 independent T0 rice transformants were generated. The primary transformants were transferred from a tissue culture chamber to a greenhouse for growing and harvest of T1 seed. Seven events, of which the T1 progeny segregated 3:1 for presence/absence of the transgene, were retained. For each of these events, approximately 10 T1 seedlings containing the transgene (hetero- and homo-zygotes) and approximately 10 T1 seedlings lacking the transgene (nullizygotes) were selected by monitoring visual marker expression. The transgenic plants and the corresponding nullizygotes were grown side-by-side at random positions. Greenhouse conditions were of shorts days (12 hours light), 28° C. in the light and 22° C. in the dark, and a relative humidity of 70%.

Four T1 events were further evaluated in the T2 generation following the same evaluation procedure as for the T1 generation but with more individuals per event. From the stage of sowing until the stage of maturity the plants were passed several times through a digital imaging cabinet. At each time point digital images (2048×1536 pixels, 16 million colours) were taken of each plant from at least 6 different angles.

5.2 Statistical Analysis: t Test and F test

A two factor ANOVA (analysis of variants) was used as a statistical model for the overall evaluation of plant phenotypic characteristics. An F test was carried out on all the parameters measured of all the plants of all the events transformed with the gene of the present invention. The F test was carried out to check for an effect of the gene over all the transformation events and to verify for an overall effect of the gene, also known as a global gene effect. The threshold for significance for a true global gene effect was set at a 5% probability level for the F test. A significant F test value points to a gene effect, meaning that it is not only the mere presence or position of the gene that is causing the differences in phenotype.

To check for an effect of the genes within an event, i.e., for a line-specific effect, a t-test was performed within each event using data sets from the transgenic plants and the corresponding null plants. “Null plants” or “null segregants” or “nullizygotes” are the plants treated in the same way as the transgenic plant, but from which the transgene has segregated. Null plants can also be described as the homozygous negative transformed plants. The threshold for significance for the t-test is set at 10% probability level. The results for some events can be above or below this threshold. This is based on the hypothesis that a gene might only have an effect in certain positions in the genome, and that the occurrence of this position-dependent effect is not uncommon. This kind of gene effect is also named herein a “line effect of the gene”. The p-value is obtained by comparing the t-value to the t-distribution or alternatively, by comparing the F-value to the F-distribution. The p-value then gives the probability that the null hypothesis (i.e., that there is no effect of the transgene) is correct.

Example 6 Evaluation Results

The mature primary panicles were harvested, counted, bagged, barcode-labeled and then dried for three days in an oven at 37° C. The panicles were then threshed and all the seeds were collected and counted. The filled husks were separated from the empty ones using an air-blowing device. The empty husks were discarded and the remaining fraction was counted again. The filled husks were weighed on an analytical balance. The number of filled seeds was determined by counting the number of filled husks that remained after the separation step. The total seed yield (total seed weight) was measured by weighing all filled husks harvested from a plant. Total seed number per plant was measured by counting the number of husks harvested from a plant. The harvest index (HI) in the present invention is defined as the ratio between the total seed yield and the above ground area (mm²), multiplied by a factor 10⁶. The total number of flowers per panicle as defined in the present invention is the ratio between the total number of seeds and the number of mature primary panicles. The seed fill rate as defined in the present invention is the proportion (expressed as a %) of the number of filled seeds over the total number of seeds (or florets).

As presented in Table B, the seed yield, number of filled seeds and harvest index are increased in the transgenic plants preferentially expressing a nucleic acid encoding a HAL3 polypeptide in the shoot, compared to control plants.

Table B shows the average yield increase (total seed weight), increase in number of filled seeds and increase of harvest index in percent, calculated from the transgenic events compared to control plants, in the T1 generation

TABLE B parameters % increase p-value Total seed weight 14 0.0072 Number of filled seeds 15 0.0052 Harvest Index 10 0.0093

Example 7 Early Vigour Evaluation Results

Early vigour was determined by counting the total number of pixels from aboveground plant parts discriminated from the background. This value was averaged for the pictures taken on the same time point from different angles and was converted to a physical surface value expressed in square mm by calibration. The results described below are for plants three weeks post-germination.

Plant early vigour (as determined by aboveground area) was seen in six out of seven events of the T1 generation, with an overall increase in aboveground area for transgenic seedlings of 27% compared to control plants. Four of these T1 events were further evaluated in the T2 generation, and all four of these events gave an increase in aboveground area for transgenic seedlings compared to control plants, with an overall increase in aboveground area for transgenic seedlings of 33% compared to control plants. The results were also shown to be statistically significant with the p-value from the F-test being lower than 0.0001 (T2 generation) indicating that the effect seen is likely due to the transgene rather than the position of the gene or a line effect, see table C.

TABLE C parameters % increase p-value Early vigour 33 0.0000

Example Section B MADS15 Upregulated Example 8 Identification of Sequences Related to SEQ ID NO: 43 and SEQ ID NO: 44

Sequences (full length cDNA, ESTs or genomic) related to SEQ ID NO: 43 and/or protein sequences related to SEQ ID NO: 44 were identified amongst those maintained in the Entrez Nucleotides database at the National Center for Biotechnology Information (NCBI) using database sequence search tools, such as the Basic Local Alignment Tool (BLAST) (Altschul et al. (1990) J. Mol. Biol. 215:403-410; and Altschul et al. (1997) Nucleic Acids Res. 25:3389-3402). The program is used to find regions of local similarity between sequences by comparing nucleic acid or polypeptide sequences to sequence databases and by calculating the statistical significance of matches. The polypeptide encoded by SEQ ID NO: 43 was used for the TBLASTN algorithm, with default settings and the filter to ignore low complexity sequences set off. The output of the analysis was viewed by pairwise comparison, and ranked according to the probability score (E-value), where the score reflects the probability that a particular alignment occurs by chance (the lower the E-value, the more significant the hit). In addition to E-values, comparisons were also scored by percentage identity. Percentage identity refers to the number of identical nucleotides (or amino acids) between the two compared nucleic acid (or polypeptide) sequences over a particular length. In some instances, the default parameters may be adjusted to modify the stringency of the search.

In addition to the publicly available nucleic acid sequences available at NCBI, proprietary sequence databases are also searched following the same procedure as described herein above.

Table D provides a list of nucleic acid and protein sequences related to the nucleic acid sequence as represented by SEQ ID NO: 43 and the protein sequence represented by SEQ ID NO: 44.

TABLE D Nucleic acid sequences related to the nucleic acid sequence (SEQ ID NO: 43) useful in the methods of the present invention, and the corresponding deduced polypeptides. database SEQ ID NO: accession name source organism nucl/protein number VRN-H1 Hordeum vulgare 52/53 AAW82995 m5 Hordeum vulgare 54/55 CAB97352 TaMADS#11 Triticum aestivum 56/57 BAA33457 TaVRT-1 Triticum aestivum 58/59 AAP33790 AP1 Triticum monococcum 60/61 AAO72630 VRN-A1 Triticum aestivum 62/63 AAW73222 MADS1 Lolium perenne 64/65 AAO45873 MADS1 Lolium temulentum 66/67 AAD10625 m15 Zea mays 68/69 CAD23408 m4 Zea mays 70/71 CAD23417 RMADS211 Oryza sativa 72/73 AAS59822 MADS14 Oryza sativa 74/75 AAF19047 Mads2 Dendrocalamus latiflorus 76/77 AAR32119 Mads1 Dendrocalamus latiflorus 78/79 AAR32118 mads3 Zea mays 80/81 AAG43200 SbMADS2 Sorghum bicolor 82/83 AAB50181 ZAP1 Zea mays 84/85 AAB00081 MADS2 Lolium temulentum 86/87 AAD10626 MADS2 Lolium perenne 88/89 AAO45874 m8 Hordeum vulgare 90/91 CAB97354 FDRMADS3 Oryza sativa 92/93 AAL09473 MADS15 Oryza sativa 94/95 AAL09473 TvFL2 Tradescantia virginiana 96/97 AAP83415 TvFL1 Tradescantia virginiana 98/99 AAP83414 TvFL3 Tradescantia virginiana 100/101 AAP83416 SQUA1 Elaeis guineensis 102/103 AAQ03221 AIFL Allium sp. 104/105 AAP83362 DOMADS2 Dendrobium grex 106/107 AAF13261

Example 9 Alignment of Relevant Polypeptide Sequences

AlignX from the Vector NTI (Invitrogen) is based on the popular Clustal algorithm of progressive alignment (Thompson et al. (1997) Nucleic Acids Res 25:4876-4882; Chema et al. (2003). Nucleic Acids Res 31:3497-3500). A phylogenetic tree can be constructed using a neighbour-joining clustering algorithm. Default values are for the gap open penalty of 10, for the gap extension penalty of 0.1 and the selected weight matrix is Blosum 62 (if polypeptides are aligned).

The result of the multiple sequence alignment using polypeptides relevant in identifying the ones useful in performing the methods of the invention is shown in FIG. 6.

Example 10 Calculation of Global Percentage Identity Between Polypeptide Sequences Useful in Performing the Methods of the Invention

Global percentages of similarity and identity between full length polypeptide sequences useful in performing the methods of the invention were determined using one of the methods available in the art, the MatGAT (Matrix Global Alignment Tool) software (BMC Bioinformatics. 2003 4:29. MatGAT: an application that generates similarity/identity matrices using protein or DNA sequences. Campanella J J, Bitincka L, Smalley J; software hosted by Ledion Bitincka). MatGAT software generates similarity/identity matrices for DNA or protein sequences without needing pre-alignment of the data. The program performs a series of pair-wise alignments using the Myers and Miller global alignment algorithm (with a gap opening penalty of 12, and a gap extension penalty of 2), calculates similarity and identity using for example Blosum 62 (for polypeptides), and then places the results in a distance matrix. Sequence similarity is shown in the bottom half of the dividing line and sequence identity is shown in the top half of the diagonal dividing line.

Parameters used in the comparison were:

-   -   Scoring matrix: Blosum62     -   First Gap: 12     -   Extending gap: 2

Results of the software analysis are shown in Table E for the global similarity and identity over the full length of the polypeptide sequences (excluding the partial polypeptide sequences). Percentage identity is given above the diagonal and percentage similarity is given below the diagonal.

The percentage identity between the polypeptide sequences useful in performing the methods of the invention can be as low as 40% amino acid identity compared to SEQ ID NO: 44.

TABLE E MatGAT results for global similarity and identity over the full length of the polypeptide sequences. 1 2 3 4 5 6 7 8 9 10 11 12 13  1. SEQID44 70.8 70.0 70.4 70.4 71.5 71.5 70.1 71.6 71.9 72.3 71.5 73.0  2. SEQID53 77.2 99.2 96.3 96.3 95.5 95.1 87.0 86.2 80.6 80.2 81.0 82.9  3. SEQID55 76.4 99.2 95.5 95.5 94.7 94.3 86.2 85.4 79.8 79.4 80.2 82.1  4. SEQID57 76.0 96.7 95.9 98.8 98.0 97.5 87.0 86.6 81.8 81.4 80.6 82.5  5. SEQID59 76.4 97.1 96.3 99.2 98.0 98.0 87.0 86.6 81.8 81.4 80.6 82.5  6. SEQID61 77.2 96.7 95.9 98.4 98.8 99.6 87.9 87.4 82.6 82.6 81.0 82.9  7. SEQID63 77.2 96.3 95.5 98.0 98.8 99.6 87.4 87.0 82.2 82.2 80.6 82.5  8. SEQID65 76.4 92.2 91.4 92.2 92.7 93.5 93.1 97.6 81.7 80.9 82.3 83.8  9. SEQID67 76.8 92.7 91.8 92.2 92.7 93.5 93.1 98.8 81.3 81.7 82.3 83.8 10. SEQID69 79.4 87.3 86.5 89.0 89.0 89.4 89.0 88.2 88.2 93.5 83.8 85.8 11. SEQID71 79.4 87.3 86.5 89.0 89.0 89.4 89.0 86.9 87.3 97.1 83.8 85.8 12. SEQID73 80.1 88.1 87.4 86.6 87.0 87.4 87.0 88.5 88.1 91.3 90.9 96.4 13. SEQID75 79.8 89.8 89.0 88.6 89.0 89.4 89.0 90.7 90.2 93.5 93.1 96.4 14. SEQID77 79.8 91.8 91.0 91.4 91.8 92.6 92.2 90.6 90.2 91.8 91.4 93.3 95.1 15. SEQID79 80.1 92.2 91.4 91.8 92.2 93.0 92.6 91.0 90.6 92.2 91.8 93.7 95.5 16. SEQID81 86.3 79.3 78.5 77.8 78.1 78.9 78.9 77.0 77.0 81.9 80.7 80.7 80.7 17. SEQID85 85.7 76.9 76.2 76.6 76.9 77.7 77.7 75.5 75.1 80.2 79.1 79.1 79.1 18. SEQID87 89.1 78.2 77.4 79.3 79.7 79.7 80.1 78.2 77.8 82.8 80.8 81.6 80.8 19. SEQID89 89.5 78.2 77.4 78.9 78.9 79.3 79.3 78.5 78.2 83.1 81.2 82.0 81.2 20. SEQID91 85.9 75.4 74.6 75.7 75.7 76.4 76.4 75.4 74.6 79.3 78.6 79.0 79.0 21. SEQID93 91.8 73.0 72.3 73.8 73.8 74.5 74.5 73.0 73.0 76.0 76.8 78.3 76.4 22. SEQID95 99.6 76.8 76.0 76.0 76.0 76.8 76.8 76.0 75.7 78.7 79.0 79.8 79.4 23. SEQID103 75.3 82.8 82.0 81.6 82.0 82.4 82.4 84.4 84.4 82.4 82.4 85.4 84.0 24. SEQID107 70.4 77.3 76.5 76.5 74.5 77.3 76.1 74.9 74.9 76.5 75.7 75.1 77.3 14 15 16 17 18 19 20 21 22 23 24  1. SEQID44 72.7 73.0 82.1 82.2 87.4 87.7 82.5 90.3 99.6 64.7 56.7  2. SEQID53 84.6 85.0 70.7 68.9 71.3 71.3 68.8 65.2 70.4 70.1 61.0  3. SEQID55 83.7 84.1 70.0 68.1 70.5 70.5 68.1 64.4 69.7 69.3 60.2  4. SEQID57 85.8 86.2 70.4 69.6 72.4 72.4 69.6 65.5 70.0 69.7 62.0  5. SEQID59 85.8 86.2 70.7 69.6 72.4 72.4 69.6 65.5 70.0 70.1 61.5  6. SEQID61 87.0 87.4 71.1 70.0 72.4 72.4 70.3 67.2 71.2 70.9 62.5  7. SEQID63 86.6 87.0 71.1 70.0 72.8 72.4 70.3 67.2 71.2 70.9 61.8  8. SEQID65 85.7 86.1 70.5 69.3 71.4 71.8 69.3 66.8 69.8 71.8 60.7  9. SEQID67 85.7 86.1 71.2 70.1 72.1 72.5 68.6 66.0 70.5 71.8 60.7 10. SEQID69 84.9 85.3 71.5 71.4 73.9 74.3 69.9 67.8 71.9 71.8 62.5 11. SEQID71 84.5 84.9 71.5 71.4 73.6 73.9 69.6 69.3 71.9 72.2 61.0 12. SEQID73 89.3 89.7 72.0 71.1 72.4 72.8 69.9 68.0 71.2 71.9 60.2 13. SEQID75 91.5 91.9 73.0 71.8 73.9 74.3 70.7 68.3 72.7 72.0 60.6 14. SEQID77 99.6 71.9 71.1 73.6 73.6 69.9 67.8 72.7 73.3 61.8 15. SEQID79 99.6 72.2 71.4 73.9 73.9 70.3 68.2 72.7 73.7 62.2 16. SEQID81 79.3 79.6 93.4 81.9 82.3 79.0 76.8 81.8 64.3 56.8 17. SEQID85 77.7 78.0 96.3 82.5 82.9 81.3 77.0 81.9 63.6 57.2 18. SEQID87 80.5 80.8 87.4 86.1 99.6 88.4 82.5 87.0 64.6 58.0 19. SEQID89 80.5 80.8 87.8 86.4 99.6 88.8 82.9 87.4 64.6 58.0 20. SEQID91 76.8 77.2 86.2 88.0 90.2 90.6 77.5 82.1 62.7 55.8 21. SEQID93 76.0 76.4 83.3 82.1 85.4 85.8 81.5 89.9 61.0 54.1 22. SEQID95 79.8 79.8 85.9 85.3 88.8 89.1 85.5 91.4 64.3 56.3 23. SEQID103 84.8 85.2 75.2 73.6 75.9 75.9 73.6 72.3 74.9 70.1 24. SEQID107 78.5 78.9 71.5 71.4 72.8 72.8 70.3 67.4 70.0 82.4

Example 11 Identification of Domains Comprised in Polypeptide Sequences Useful in Performing the Methods of the Invention

The Integrated Resource of Protein Families, Domains and Sites (InterPro) database is an integrated interface for the commonly used signature databases for text- and sequence-based searches. The InterPro database combines these databases, which use different methodologies and varying degrees of biological information about well-characterized proteins to derive protein signatures. Collaborating databases include SWISS-PROT, PROSITE, TrEMBL, PRINTS, Propom and Pfam, Smart and TIGRFAMs. Interpro is hosted at the European Bioinformatics Institute in the United Kingdom.

The results of the InterPro scan of the polypeptide sequence as represented by SEQ ID NO: 44 are presented in Table F.

TABLE F InterPro scan results of the polypeptide sequence as represented by SEQ ID NO: 44 Database Accession number Accession name PRINTS PR00404 MADSDOMAIN PFAM PF00319 SRF-TF SMART SM00432 MADS PROFILE PS50066 MADS_BOX_2 SUPERFAMILY SSF55455 SRF-like PFAM PF01486 K-box SUPERFAMILY SSF46589 tRNA-binding arm PANTHER PTHR11945 MADS BOX PROTEIN PANTHER PTHR11945:SF19 MADS BOX PROTEIN

Example 12 Topology Prediction of the Polypeptide Sequences Useful in Performing the Methods of the Invention (Subcellular Localization, Transmembrane . . . )

TargetP 1.1 predicts the subcellular location of eukaryotic proteins. The location assignment is based on the predicted presence of any of the N-terminal pre-sequences: chloroplast transit peptide (cTP), mitochondrial targeting peptide (mTP) or secretory pathway signal peptide (SP). Scores on which the final prediction is based are not really probabilities, and they do not necessarily add to one. However, the location with the highest score is the most likely according to TargetP, and the relationship between the scores (the reliability class) may be an indication of how certain the prediction is. The reliability class (RC) ranges from 1 to 5, where 1 indicates the strongest prediction. TargetP is maintained at the server of the Technical University of Denmark.

For the sequences predicted to contain an N-terminal presequence a potential cleavage site can also be predicted.

A number of parameters were selected, such as organism group (non-plant or plant), cutoff sets (none, predefined set of cutoffs, or user-specified set of cutoffs), and the calculation of prediction of cleavage sites (yes or no).

The results of TargetP 1.1 analysis of the polypeptide sequence as represented by SEQ ID NO: 44 are presented Table G. The “plant” organism group has been selected, no cutoffs defined, and the predicted length of the transit peptide requested. The subcellular localization of the polypeptide sequence as represented by SEQ ID NO: 44 may be the cytoplasm or nucleus, no transit peptide is predicted.

TABLE G TargetP 1.1 analysis of the polypeptide sequence as represented by SEQ ID NO: 44 Length (AA) 267 Chloroplastic transit peptide 0.088 Mitochondrial transit peptide 0.492 Secretory pathway signal peptide 0.046 Other subcellular targeting 0.655 Predicted Location Chloroplastic Reliability class 5 Predicted transit peptide length /

Many other algorithms can be used to perform such analyses, including:

-   -   ChloroP 1.1 hosted on the server of the Technical University of         Denmark;     -   Protein Prowler Subcellular Localisation Predictor version 1.2         hosted on the server of the Institute for Molecular Bioscience,         University of Queensland, Brisbane, Australia;     -   PENCE Proteome Analyst PA-GOSUB 2.5 hosted on the server of the         University of Alberta, Edmonton, Alberta, Canada;     -   TMHMM, hosted on the server of the Technical University of         Denmark

Example 13 Assay Related to the Polypeptide Sequences Useful in Performing the Methods of the Invention

Lim et al. (PMB 44, 513-527, 2000) describe two assays for measuring protein-protein interactions that may be applied to MADS15. In the yeast two-hybrid assay, a truncated form of MADS1 (comprising the complete MADS box, the I- and K-domain but lacking the C-terminal part of the C-domain) was used as bait to test interaction with MADS15. In the in vitro pull-down assay, GST and GST-fused MADS1 proteins were produced and immobilised on glutathione Sepharose 4B. The resin-bound GST/GST-MADS1 was mixed with ³⁵S-labeled MADS15 proteins or fragments thereof. After washing, the interacting proteins were eluted and analysed by SDS-PAGE. A person skilled in the art will appreciate that the MADS15 protein may be used as bait in the two-hybrid screen or may be immobilised on glutathione resin as well. Furthermore, a MADS15 protein, when used according to the methods of the present invention, will result in increased root yield in rice, measured as an increased ratio of root biomass over shoot biomass.

Example 14 Cloning of Nucleic Acid Sequence as Represented by SEQ ID NO: 43

The Oryza sativa MADS15 gene was amplified by PCR using as template an Oryza sativa seedling cDNA library (Invitrogen, Paisley, UK). After reverse transcription of RNA extracted from seedlings, the cDNAs were cloned into pCMV Sport 6.0. Average insert size of the bank was 1.5 kb and the original number of clones was of the order of 1.59×10⁷ cfu. Original titer was determined to be 9.6×10⁵ cfu/ml after first amplification of 6×10¹¹ cfu/ml. After plasmid extraction, 200 ng of template was used in a 50 μl PCR mix. Primers prm06892 (SEQ ID NO: 45; sense, start codon in bold, AttB1 site in italic: 5′-ggggacaagtttgtacaaaaaagcaggcttaaaca atgggcgggggaaggt-3′) and prm06893 (SEQ ID NO: 46; reverse, complementary, AttB2 site in italic: 5′-ggggaccactttgtacaagaaagctgggtttggccgacgacgacgac-3′), which include the AttB sites for Gateway recombination, were used for PCR amplification. PCR was performed using Hifi Taq DNA polymerase in standard conditions. A PCR fragment of around 915 bp was amplified and purified also using standard methods. The first step of the Gateway procedure, the BP reaction, was then performed, during which the PCR fragment recombines in vivo with the pDONR201 plasmid to produce, according to the Gateway terminology, an “entry clone”, pMADS15. Plasmid pDONR201 was purchased from Invitrogen, as part of the Gateway® technology.

Example 15 Expression Vector Construction Using the Nucleic Acid Sequence as Represented by SEQ ID NO: 43

The entry clone pMADS15 was subsequently used in an LR reaction with pGOS2, a destination vector used for Oryza sativa transformation. This vector contains as functional elements within the T-DNA borders: a plant selectable marker; a screenable marker expression cassette; and a Gateway cassette intended for LR in vivo recombination with the nucleic acid sequence of interest already cloned in the entry clone. A rice GOS2 promoter (SEQ ID NO: 108, alternatively, SEQ ID NO: 47 is equally useful) for constitutive expression was located upstream of this Gateway cassette.

After the LR recombination step, the resulting expression vector pGOS2::MADS15 (FIG. 7) was transformed into Agrobacterium strain LBA4044 according to methods well known in the art.

Example 16 Plant Transformation Rice Transformation

The Agrobacterium containing the expression vector was used to transform Oryza sativa plants. Mature dry seeds of the rice japonica cultivar Nipponbare were dehusked. Sterilization was carried out by incubating for one minute in 70% ethanol, followed by 30 minutes in 0.2% HgCl₂, followed by a 6 times 15 minutes wash with sterile distilled water. The sterile seeds were then germinated on a medium containing 2,4-D (callus induction medium). After incubation in the dark for four weeks, embryogenic, scutellum-derived calli were excised and propagated on the same medium. After two weeks, the calli were multiplied or propagated by subculture on the same medium for another 2 weeks. Embryogenic callus pieces were sub-cultured on fresh medium 3 days before co-cultivation (to boost cell division activity).

Agrobacterium strain LBA4404 containing the expression vector was used for co-cultivation. Agrobacterium was inoculated on AB medium with the appropriate antibiotics and cultured for 3 days at 28° C. The bacteria were then collected and suspended in liquid co-cultivation medium to a density (OD₆₀₀) of about 1. The suspension was then transferred to a Petri dish and the calli immersed in the suspension for 15 minutes. The callus tissues were then blotted dry on a filter paper and transferred to solidified, co-cultivation medium and incubated for 3 days in the dark at 25° C. Co-cultivated calli were grown on 2,4-D-containing medium for 4 weeks in the dark at 28° C. in the presence of a selection agent. During this period, rapidly growing resistant callus islands developed. After transfer of this material to a regeneration medium and incubation in the light, the embryogenic potential was released and shoots developed in the next four to five weeks. Shoots were excised from the calli and incubated for 2 to 3 weeks on an auxin-containing medium from which they were transferred to soil. Hardened shoots were grown under high humidity and short days in a greenhouse.

The primary transformants were transferred from a tissue culture chamber to a greenhouse. After a quantitative PCR analysis to verify copy number of the T-DNA insert, only single copy transgenic plants that exhibit tolerance to the selection agent were kept for harvest of T1 seed. Seeds were then harvested three to five months after transplanting. The method yielded single locus transformants at a rate of over 50% (Aldemita and Hodges1996, Chan et al. 1993, Hiei et al. 1994).

Corn Transformation

Transformation of maize (Zea mays) Is performed with a modification of the method described by Ishida et al. (1996) Nature Biotech 14(6): 745-50. Transformation is genotype-dependent in corn and only specific genotypes are amenable to transformation and regeneration. The inbred line A188 (University of Minnesota) or hybrids with A188 as a parent are good sources of donor material for transformation, but other genotypes can be used successfully as well. Ears are harvested from corn plant approximately 11 days after pollination (DAP) when the length of the immature embryo is about 1 to 1.2 mm. Immature embryos are cocultivated with Agrobacterium tumefaciens containing the expression vector, and transgenic plants are recovered through organogenesis. Excised embryos are grown on callus induction medium, then maize regeneration medium, containing the selection agent (for example imidazolinone but various selection markers can be used). The Petri plates are incubated in the light at 25° C. for 2-3 weeks, or until shoots develop. The green shoots are transferred from each embryo to maize rooting medium and incubated at 25° C. for 2-3 weeks, until roots develop. The rooted shoots are transplanted to soil in the greenhouse. T1 seeds are produced from plants that exhibit tolerance to the selection agent and that contain a single copy of the T-DNA insert.

Wheat Transformation

Transformation of wheat is performed with the method described by Ishida et al. (1996) Nature Biotech 14(6): 745-50. The cultivar Bobwhite (available from CIMMYT, Mexico) is commonly used in transformation. Immature embryos are co-cultivated with Agrobacterium tumefaciens containing the expression vector, and transgenic plants are recovered through organogenesis. After incubation with Agrobacterium, the embryos are grown in vitro on callus induction medium, then regeneration medium, containing the selection agent (for example imidazolinone but various selection markers can be used). The Petri plates are incubated in the light at 25° C. for 2-3 weeks, or until shoots develop. The green shoots are transferred from each embryo to rooting medium and incubated at 25° C. for 2-3 weeks, until roots develop. The rooted shoots are transplanted to soil in the greenhouse. T1 seeds are produced from plants that exhibit tolerance to the selection agent and that contain a single copy of the T-DNA insert.

Soybean Transformation

Soybean is transformed according to a modification of the method described in the Texas A&M U.S. Pat. No. 5,164,310. Several commercial soybean varieties are amenable to transformation by this method. The cultivar Jack (available from the Illinois Seed foundation) is commonly used for transformation. Soybean seeds are sterilised for in vitro sowing. The hypocotyl, the radicle and one cotyledon are excised from seven-day old young seedlings. The epicotyl and the remaining cotyledon are further grown to develop axillary nodes. These axillary nodes are excised and incubated with Agrobacterium tumefaciens containing the expression vector. After the cocultivation treatment, the explants are washed and transferred to selection media. Regenerated shoots are excised and placed on a shoot elongation medium. Shoots no longer than 1 cm are placed on rooting medium until roots develop. The rooted shoots are transplanted to soil in the greenhouse. T1 seeds are produced from plants that exhibit tolerance to the selection agent and that contain a single copy of the T-DNA insert.

Rapeseed/Canola Transformation

Cotyledonary petioles and hypocotyls of 5-6 day old young seedling are used as explants for tissue culture and transformed according to Babic et al. (1998, Plant Cell Rep 17: 183-188). The commercial cultivar Westar (Agriculture Canada) is the standard variety used for transformation, but other varieties can also be used. Canola seeds are surface-sterilized for in vitro sowing. The cotyledon petiole explants with the cotyledon attached are excised from the in vitro seedlings, and inoculated with Agrobacterium (containing the expression vector) by dipping the cut end of the petiole explant into the bacterial suspension. The explants are then cultured for 2 days on MSBAP-3 medium containing 3 mg/l BAP, 3% sucrose, 0.7% Phytagar at 23° C., 16 hr light. After two days of co-cultivation with Agrobacterium, the petiole explants are transferred to MSBAP-3 medium containing 3 mg/l BAP, cefotaxime, carbenicillin, or timentin (300 mg/l) for 7 days, and then cultured on MSBAP-3 medium with cefotaxime, carbenicillin, or timentin and selection agent until shoot regeneration. When the shoots are 5-10 mm in length, they are cut and transferred to shoot elongation medium (MSBAP-0.5, containing 0.5 mg/l BAP). Shoots of about 2 cm in length are transferred to the rooting medium (MS0) for root induction. The rooted shoots are transplanted to soil in the greenhouse. T1 seeds are produced from plants that exhibit tolerance to the selection agent and that contain a single copy of the T-DNA insert.

Alfalfa Transformation

A regenerating clone of alfalfa (Medicago sativa) is transformed using the method of (McKersie et al., 1999 Plant Physiol 119: 839-847). Regeneration and transformation of alfalfa is genotype dependent and therefore a regenerating plant is required. Methods to obtain regenerating plants have been described. For example, these can be selected from the cultivar Rangelander (Agriculture Canada) or any other commercial alfalfa variety as described by Brown D C W and A Atanassov (1985. Plant Cell Tissue Organ Culture 4: 111-112). Alternatively, the RA3 variety (University of Wisconsin) has been selected for use in tissue culture (Walker et al., 1978 Am J Bot 65:654-659). Petiole explants are cocultivated with an overnight culture of Agrobacterium tumefaciens C58C1 pMP90 (McKersie et al., 1999 Plant Physiol 119: 839-847) or LBA4404 containing the expression vector. The explants are cocultivated for 3 d in the dark on SH induction medium containing 288 mg/L Pro, 53 mg/L thioproline, 4.35 g/L K2SO4, and 100 μm acetosyringinone. The explants are washed in half-strength Murashige-Skoog medium (Murashige and Skoog, 1962) and plated on the same SH induction medium without acetosyringinone but with a suitable selection agent and suitable antibiotic to inhibit Agrobacterium growth. After several weeks, somatic embryos are transferred to BOi2Y development medium containing no growth regulators, no antibiotics, and 50 g/L sucrose. Somatic embryos are subsequently germinated on half-strength Murashige-Skoog medium. Rooted seedlings were transplanted into pots and grown in a greenhouse. T1 seeds are produced from plants that exhibit tolerance to the selection agent and that contain a single copy of the T-DNA insert.

Example 17 Phenotypic Evaluation Procedure 17.1 Evaluation Setup

Approximately 35 independent TO rice transformants were generated. The primary transformants were transferred from a tissue culture chamber to a greenhouse for growing and harvest of T1 seed. Six events, of which the T1 progeny segregated 3:1 for presence/absence of the transgene, were retained. For each of these events, approximately 10 T1 seedlings containing the transgene (hetero- and homo-zygotes) and approximately 10 T1 seedlings lacking the transgene (nullizygotes) were selected by monitoring visual marker expression. The transgenic plants and the corresponding nullizygotes were grown side-by-side at random positions. Greenhouse conditions were of shorts days (12 hours light), 28° C. in the light and 22° C. in the dark, and a relative humidity of 70%.

Four T1 events were further evaluated in the T2 generation following the same evaluation procedure as for the T1 generation but with more individuals per event. From the stage of sowing until the stage of maturity the plants were passed several times through a digital imaging cabinet. At each time point digital images (2048×1536 pixels, 16 million colours) were taken of each plant from at least 6 different angles.

17.2 Statistical Analysis: F-Test

A two factor ANOVA (analysis of variants) was used as a statistical model for the overall evaluation of plant phenotypic characteristics. An F-test was carried out on all the parameters measured of all the plants of all the events transformed with the gene of the present invention. The F-test was carried out to check for an effect of the gene over all the transformation events and to verify for an overall effect of the gene, also known as a global gene effect. The threshold for significance for a true global gene effect was set at a 5% probability level for the F-test. A significant F-test value points to a gene effect, meaning that it is not only the mere presence or position of the gene that is causing the differences in phenotype.

To check for an effect of the genes within an event, i.e., for a line-specific effect, a t-test was performed within each event using data sets from the transgenic plants and the corresponding null plants. “Null plants” or “null segregants” or “nullizygotes” are the plants treated in the same way as the transgenic plant, but from which the transgene has segregated. Null plants can also be described as the homozygous negative transformed plants. The threshold for significance for the t-test is set at 10% probability level. The results for some events can be above or below this threshold. This is based on the hypothesis that a gene might only have an effect in certain positions in the genome, and that the occurrence of this position-dependent effect is not uncommon. This kind of gene effect is also named herein a “line effect of the gene”. The p-value is obtained by comparing the t-value to the t-distribution or alternatively, by comparing the F-value to the F-distribution. The p-value then gives the probability that the null hypothesis (i.e., that there is no effect of the transgene) is correct.

17.3 Parameters Measured

From the stage of sowing until the stage of maturity the plants were passed several times through a digital imaging cabinet. At each time point digital images (2048×1536 pixels, 16 million colours) were taken of each plant from at least 6 different angles.

The plant aboveground area (or leafy biomass) was determined by counting the total number of pixels on the digital images from aboveground plant parts discriminated from the background. This value was averaged for the pictures taken on the same time point from the different angles and was converted to a physical surface value expressed in square mm by calibration. Experiments show that the aboveground plant area measured this way correlates with the biomass of plant parts above ground. The above ground area is the area measured at the time point at which the plant had reached its maximal leafy biomass. The early vigour is the plant (seedling) aboveground area three weeks post-germination. Increase in root biomass is expressed as an increase in total root biomass (measured as maximum biomass of roots observed during the lifespan of a plant); or as an increase in the root/shoot index (measured as the ratio between root biomass and shoot biomass in the period of active growth of root and shoot).

Example 18 Results of the Phenotypic Evaluation of the Transgenic Plants

Upon analysis of the plants as described above, the inventors found that plants transformed with the MADS15 gene construct had a higher root yield, expressed as root/shoot index, compared to plants lacking the MADS15 transgene. The increase was 9.4% (p-value 0.0207) in T1 and 25.7% (p-value 0.0002) in T2. The p-values show that the increases were significant.

Example Section C MADS15 Down-Regulated

See also Examples 8 to 13 for the identification and characterisation of MADS15 related sequences.

Example 19 Gene Cloning

The Oryza sativa MADS15 gene was amplified by PCR using as template an Oryza sativa seedling cDNA library (Invitrogen, Paisley, UK). After reverse transcription of RNA extracted from seedlings, the cDNAs were cloned into pCMV Sport 6.0. Average insert size of the bank was 1.5 kb and the original number of clones was of the order of 1.59×10⁷ cfu. Original titer was determined to be 9.6×10⁵ cfu/ml after first amplification of 6×10¹¹ cfu/ml. After plasmid extraction, 200 ng of template was used in a 50 μl PCR mix. Primers prm06892 (SEQ ID NO: 111; sense, start codon in bold, AttB1 site in italic: ′-ggggacaagtttgtacaaaaaagcaggcttaaacaatggg cgggggaaggt-3′) and prm06893 (SEQ ID NO: 112; reverse, complementary, AttB2 site in italic: 5′-ggggaccactttgtacaagaaagctgggtttggccgacgacgacgac-3′), which include the AttB sites for Gateway recombination, were used for PCR amplification. PCR was performed using Hifi Taq DNA polymerase in standard conditions. A PCR fragment of around 915 bp was amplified and purified also using standard methods. The PCR fragment was subsequently used for the preparation of a hairpin construct, using techniques known in the art. The first step of the Gateway procedure, the BP reaction, was then performed, during which the hairpin construct recombines in vivo with the pDONR201 plasmid to produce, according to the Gateway terminology, an “entry clone”, pMADS15hp. Plasmid pDONR201 was purchased from Invitrogen, as part of the Gateway® technology.

Example 20 Vector Construction

The entry clone pMADS15hp was subsequently used in an LR reaction with p01519, a destination vector for the inverted repeat construct. This vector contains as functional elements within the T-DNA borders: a plant selectable marker; a screenable marker expression cassette; and a Gateway cassette intended for LR in vivo recombination such that the sequence of interest from the entry clone is integrated as an inverted repeat. A rice GOS2 promoter (SEQ ID NO: 174, alternatively, SEQ ID NO: 113 is equally useful) for constitutive expression was located upstream of this Gateway cassette.

After the LR recombination step, the resulting expression vector with the inverted repeat, FIG. 10) were transformed into Agrobacterium strain LBA4044 and subsequently to Oryza sativa plants.

Example 21 Plant Transformation Rice Transformation

The Agrobacterium containing the expression vector was used to transform Oryza sativa plants. Mature dry seeds of the rice japonica cultivar Nipponbare were dehusked. Sterilization was carried out by incubating for one minute in 70% ethanol, followed by 30 minutes in 0.2% HgCl₂, followed by a 6 times 15 minutes wash with sterile distilled water. The sterile seeds were then germinated on a medium containing 2,4-D (callus induction medium). After incubation in the dark for four weeks, embryogenic, scutellum-derived calli were excised and propagated on the same medium. After two weeks, the calli were multiplied or propagated by subculture on the same medium for another 2 weeks. Embryogenic callus pieces were sub-cultured on fresh medium 3 days before co-cultivation (to boost cell division activity).

Agrobacterium strain LBA4404 containing the expression vector was used for co-cultivation. Agrobacterium was inoculated on AB medium with the appropriate antibiotics and cultured for 3 days at 28° C. The bacteria were then collected and suspended in liquid co-cultivation medium to a density (OD₆₀₀) of about 1. The suspension was then transferred to a Petri dish and the calli immersed in the suspension for 15 minutes. The callus tissues were then blotted dry on a filter paper and transferred to solidified, co-cultivation medium and incubated for 3 days in the dark at 25° C. Co-cultivated calli were grown on 2,4-D-containing medium for 4 weeks in the dark at 28° C. in the presence of a selection agent. During this period, rapidly growing resistant callus islands developed. After transfer of this material to a regeneration medium and incubation in the light, the embryogenic potential was released and shoots developed in the next four to five weeks. Shoots were excised from the calli and incubated for 2 to 3 weeks on an auxin-containing medium from which they were transferred to soil. Hardened shoots were grown under high humidity and short days in a greenhouse.

The primary transformants were transferred from a tissue culture chamber to a greenhouse. After a quantitative PCR analysis to verify copy number of the T-DNA insert, only single copy transgenic plants that exhibit tolerance to the selection agent were kept for harvest of T1 seed.

Seeds were then harvested three to five months after transplanting. The method yielded single locus transformants at a rate of over 50% (Aldemita and Hodges1996, Chan et al. 1993, Hiei et al. 1994).

Corn Transformation

Transformation of maize (Zea mays) is performed with a modification of the method described by Ishida et al. (1996) Nature Biotech 14(6): 745-50. Transformation is genotype-dependent in corn and only specific genotypes are amenable to transformation and regeneration. The inbred line A188 (University of Minnesota) or hybrids with A188 as a parent are good sources of donor material for transformation, but other genotypes can be used successfully as well. Ears are harvested from corn plant approximately 11 days after pollination (DAP) when the length of the immature embryo is about 1 to 1.2 mm. Immature embryos are cocultivated with Agrobacterium tumefaciens containing the expression vector, and transgenic plants are recovered through organogenesis. Excised embryos are grown on callus induction medium, then maize regeneration medium, containing the selection agent (for example imidazolinone but various selection markers can be used). The Petri plates are incubated in the light at 25° C. for 2-3 weeks, or until shoots develop. The green shoots are transferred from each embryo to maize rooting medium and incubated at 25° C. for 2-3 weeks, until roots develop. The rooted shoots are transplanted to soil in the greenhouse. T1 seeds are produced from plants that exhibit tolerance to the selection agent and that contain a single copy of the T-DNA insert.

Wheat Transformation

Transformation of wheat is performed with the method described by Ishida et al. (1996) Nature Biotech 14(6): 745-50. The cultivar Bobwhite (available from CIMMYT, Mexico) is commonly used in transformation. Immature embryos are co-cultivated with Agrobacterium tumefaciens containing the expression vector, and transgenic plants are recovered through organogenesis. After incubation with Agrobacterium, the embryos are grown in vitro on callus induction medium, then regeneration medium, containing the selection agent (for example imidazolinone but various selection markers can be used). The Petri plates are incubated in the light at 25° C. for 2-3 weeks, or until shoots develop. The green shoots are transferred from each embryo to rooting medium and incubated at 25° C. for 2-3 weeks, until roots develop. The rooted shoots are transplanted to soil in the greenhouse. T1 seeds are produced from plants that exhibit tolerance to the selection agent and that contain a single copy of the T-DNA insert.

Soybean Transformation

Soybean is transformed according to a modification of the method described in the Texas A&M U.S. Pat. No. 5,164,310. Several commercial soybean varieties are amenable to transformation by this method. The cultivar Jack (available from the Illinois Seed foundation) is commonly used for transformation. Soybean seeds are sterilised for in vitro sowing. The hypocotyl, the radicle and one cotyledon are excised from seven-day old young seedlings. The epicotyl and the remaining cotyledon are further grown to develop axillary nodes. These axillary nodes are excised and incubated with Agrobacterium tumefaciens containing the expression vector. After the cocultivation treatment, the explants are washed and transferred to selection media. Regenerated shoots are excised and placed on a shoot elongation medium. Shoots no longer than 1 cm are placed on rooting medium until roots develop. The rooted shoots are transplanted to soil in the greenhouse. T1 seeds are produced from plants that exhibit tolerance to the selection agent and that contain a single copy of the T-DNA insert.

Rapeseed/Canola Transformation

Cotyledonary petioles and hypocotyls of 5-6 day old young seedling are used as explants for tissue culture and transformed according to Babic et al. (1998, Plant Cell Rep 17: 183-188). The commercial cultivar Westar (Agriculture Canada) is the standard variety used for transformation, but other varieties can also be used. Canola seeds are surface-sterilized for in vitro sowing. The cotyledon petiole explants with the cotyledon attached are excised from the in vitro seedlings, and inoculated with Agrobacterium (containing the expression vector) by dipping the cut end of the petiole explant into the bacterial suspension. The explants are then cultured for 2 days on MSBAP-3 medium containing 3 mg/l BAP, 3% sucrose, 0.7% Phytagar at 23° C., 16 hr light. After two days of co-cultivation with Agrobacterium, the petiole explants are transferred to MSBAP-3 medium containing 3 mg/l BAP, cefotaxime, carbenicillin, or timentin (300 mg/l) for 7 days, and then cultured on MSBAP-3 medium with cefotaxime, carbenicillin, or timentin and selection agent until shoot regeneration. When the shoots are 5-10 mm in length, they are cut and transferred to shoot elongation medium (MSBAP-0.5, containing 0.5 mg/l BAP). Shoots of about 2 cm in length are transferred to the rooting medium (MS0) for root induction. The rooted shoots are transplanted to soil in the greenhouse. T1 seeds are produced from plants that exhibit tolerance to the selection agent and that contain a single copy of the T-DNA insert.

Alfalfa Transformation

A regenerating clone of alfalfa (Medicago sativa) is transformed using the method of (McKersie et al., 1999 Plant Physiol 119: 839-847). Regeneration and transformation of alfalfa is genotype dependent and therefore a regenerating plant is required. Methods to obtain regenerating plants have been described. For example, these can be selected from the cultivar Rangelander (Agriculture Canada) or any other commercial alfalfa variety as described by Brown D C W and A Atanassov (1985. Plant Cell Tissue Organ Culture 4: 111-112). Alternatively, the RA3 variety (University of Wisconsin) has been selected for use in tissue culture (Walker et al., 1978 Am J Bot 65:654-659). Petiole explants are cocultivated with an overnight culture of Agrobacterium tumefaciens C58C1 pMP90 (McKersie et al., 1999 Plant Physiol 119: 839-847) or LBA4404 containing the expression vector. The explants are cocultivated for 3 d in the dark on SH induction medium containing 288 mg/L Pro, 53 mg/L thioproline, 4.35 g/L K2SO4, and 100 μm acetosyringinone. The explants are washed in half-strength Murashige-Skoog medium (Murashige and Skoog, 1962) and plated on the same SH induction medium without acetosyringinone but with a suitable selection agent and suitable antibiotic to inhibit Agrobacterium growth. After several weeks, somatic embryos are transferred to BOi2Y development medium containing no growth regulators, no antibiotics, and 50 g/L sucrose. Somatic embryos are subsequently germinated on half-strength Murashige-Skoog medium. Rooted seedlings were transplanted into pots and grown in a greenhouse. T1 seeds are produced from plants that exhibit tolerance to the selection agent and that contain a single copy of the T-DNA insert.

Example 22 Evaluation Methods of Plants Transformed with the MADS15 Inverted Repeat Under Control of the Rice GOS2 Promoter

Approximately 15 to 20 independent T0 rice transformants were generated. The primary transformants were transferred from a tissue culture chamber to a greenhouse for growing and harvest of T1 seed. Eight events for the inverted repeat construct of which the T1 progeny segregated 3:1 for presence/absence of the transgene, were retained. For each of these events, approximately 10 T1 seedlings containing the transgene (hetero- and homozygotes) and approximately 10 T1 seedlings lacking the transgene (nullizygotes) were selected by monitoring visual marker expression. The selected T1 plants were transferred to a greenhouse. Each plant received a unique barcode label to link unambiguously the phenotyping data to the corresponding plant. The selected T1 plants were grown on soil in 10 cm diameter pots under the following environmental settings: photoperiod=11.5 h, daylight intensity=30,000 lux or more, daytime temperature=28° C. or higher, night time temperature=22° C., relative humidity=60-70%. Transgenic plants and the corresponding nullizygotes were grown side-by-side at random positions. From the stage of sowing until the stage of maturity the plants were passed several times through a digital imaging cabinet. At each time point digital images (2048×1536 pixels, 16 million colours) were taken of each plant from at least 6 different angles.

The plant aboveground area (or leafy biomass) was determined by counting the total number of pixels on the digital images from aboveground plant parts discriminated from the background. This value was averaged for the pictures taken on the same time point from the different angles and was converted to a physical surface value expressed in square mm by calibration. Experiments show that the aboveground plant area measured this way correlates with the biomass of plant parts above ground. The Areamax is the above ground area at the time point at which the plant had reached its maximal leafy biomass.

The mature primary panicles were harvested, bagged, barcode-labelled and then dried for three days in the oven at 37° C. The panicles were then threshed and all the seeds collected. The filled husks were separated from the empty ones using an air-blowing device. After separation, both seed lots were then counted using a commercially available counting machine. The empty husks were discarded. The filled husks were weighed on an analytical balance and the cross-sectional area of the seeds was measured using digital imaging. This procedure resulted in the set of the following seed-related parameters:

The flowers-per-panicle is a parameter estimating the average number of florets per panicle on a plant, derived from the number of total seeds divided by the number of first panicles. The tallest panicle and all the panicles that overlapped with the tallest panicle when aligned vertically, were considered as first panicles and were counted manually. The number of filled seeds was determined by counting the number of filled husks that remained after the separation step. The total seed yield (total seed weight) was measured by weighing all filled husks harvested from a plant. Total seed number per plant was measured by counting the number of husks harvested from a plant and corresponds to the number of florets per plant. These parameters were derived in an automated way from the digital images using image analysis software and were analysed statistically. Individual seed parameters (including width, length, area, weight) were measured using a custom-made device consisting of two main components, a weighing and imaging device, coupled to software for image analysis.

A two factor ANOVA (analyses of variance) corrected for the unbalanced design was used as statistical model for the overall evaluation of plant phenotypic characteristics. An F-test was carried out on all the parameters measured of all the plants of all the events transformed with that gene. The F-test was carried out to check for an effect of the gene over all the transformation events and to verify for an overall effect of the gene, also named herein “global gene effect”. If the value of the F test shows that the data are significant, than it is concluded that there is a “gene” effect, meaning that not only presence or the position of the gene is causing the effect. The threshold for significance for a true global gene effect is set at 5% probability level for the F test.

To check for an effect of the genes within an event, i.e., for a line-specific effect, a t-test was performed within each event using data sets from the transgenic plants and the corresponding null plants. “Null plants” or “null segregants” or “nullizygotes” are the plants treated in the same way as the transgenic plant, but from which the transgene has segregated. Null plants can also be described as the homozygous negative transformed plants. The threshold for significance for the t-test is set at 10% probability level. The results for some events can be above or below this threshold. This is based on the hypothesis that a gene might only have an effect in certain positions in the genome, and that the occurrence of this position-dependent effect is not uncommon. This kind of gene effect is also named herein a “line effect of the gene”. The p-value is obtained by comparing the t-value to the t-distribution or alternatively, by comparing the F-value to the F-distribution. The p-value then gives the probability that the null hypothesis (i.e., that there is no effect of the transgene) is correct.

Example 23 Measurement of Yield-Related Parameters for the Inverted Repeat Construct Transformants

Upon analysis of the seeds as described above, the inventors found that plants transformed with the hairpin MADS15 gene construct had a higher seed yield, expressed as number of filled seeds, total weight of seeds, total number of seeds, and flowers per panicle, compared to plants lacking the MADS15 transgene, whereas the plants transformed with the sense MADS15 gene construct showed opposite effects. The p-values show that the increases were significant.

The results obtained for plants in the T1 generation are summarised in Table H, which represent the mean values for all the tested lines:

TABLE H % difference p-value number of filled seeds +122 0.0000 total weight of seeds +112 0.0000 total number of seeds +27 0.0000 flowers per panicle +25 0.0000

Example Section D PLT Example 24 Identification of Sequences Related to the Nucleic Acid Sequence Used in the Methods of the Invention

Sequences (full length cDNA, ESTs or genomic) related to the nucleic acid sequence used in the methods of the present invention were identified amongst those maintained in the Entrez Nucleotides database at the National Center for Biotechnology Information (NCBI) using database sequence search tools, such as the Basic Local Alignment Tool (BLAST) (Altschul et al. (1990) J. Mol. Biol. 215:403-410; and Altschul et al. (1997) Nucleic Acids Res. 25:3389-3402). The program is used to find regions of local similarity between sequences by comparing nucleic acid or polypeptide sequences to sequence databases and by calculating the statistical significance of matches. For example, the polypeptide encoded by the nucleic acid of the present invention was used for the TBLASTN algorithm, with default settings and the filter to ignore low complexity sequences set off. The output of the analysis was viewed by pairwise comparison, and ranked according to the probability score (E-value), where the score reflect the probability that a particular alignment occurs by chance (the lower the E-value, the more significant the hit). In addition to E-values, comparisons were also scored by percentage identity. Percentage identity refers to the number of identical nucleotides (or amino acids) between the two compared nucleic acid (or polypeptide) sequences over a particular length. In some instances, the default parameters may be adjusted to modify the stringency of the search. For example the E-value may be increased to show less stringent matches. This way, short nearly exact matches may be identified.

The Table I below provides a list of nucleic acid sequences related to the nucleic acid sequence used in the methods of the present invention.

TABLE I nucleic acid sequences related to the nucleic acid sequence used in the methods of the present invention Nucleic acid Polypeptide NCBI accession Name SEQ ID NO SEQ ID NO number Source organism Arath_PLT1 175 176 full length NM_112975 Arabidopsis thaliana (At3g20840) Arath_PLT2 177 178 full length NM_103997 Arabidopsis thaliana (At1g51190) Glyma_PLT 179 180 full length BU964973.1 Glycine max CA783156.1 BM309051.1 BM309377.1 Glyma_PLT2 181 182 full length BU926204.1 Glycine max BU547204.1 CA783156.1 BU927164.1 Medtr_PLT 183 184 full length AC144930.20 Medicago truncatula Orysa_PLT 185 186 full length NM_190301 Oryza sativa Zeama_PLT 187 188 full length CS155772.1 Zea mays Lotco_PLT 189 190 partial AP007400 Lotus corniculatus Poptr_PLT I 199 200 full length scaff_III.1595 Populus tremuloides Poptr_PLT II 201 202 full length scaff_I.328 Populus tremuloides Vitvi_PLT 203 204 partial AM469514 Vitis vinifera Brana_PLT 205 206 partial CN730825 Brassica napus Phaco_PLT 207 208 partial CA902624.1| Phaseolus coccineus

In some instances, related sequences have tentatively been assembled and publicly disclosed by research institutions, such as The Institute for Genomic Research (TIGR). The Eukaryotic Gene Orthologs (EGO) database may be used to identify such related sequences, either by keyword search or by using the BLAST algorithm with the nucleic acid or polypeptide sequence of interest.

Example 25 Cloning of the Nucleic Acid Sequences Used in the Methods of the Invention

The nucleic acid sequences used in the methods of the invention were amplified by PCR using as template a custom-made Arabidopsis thaliana cDNA library made starting from RNA extracted from different tissues (in pCMV Sport 6.0; Invitrogen, Paisley, UK). PCR was performed using Hifi Taq DNA polymerase in standard conditions, using 200 ng of template in a 50 μl PCR mix. The primers used to amplify SEQ ID NO: 175 (PLT1) were prm08180 (SEQ ID NO: 195; sense, start codon in bold, AttB1 site in italic: 5′ GGGGACAAGTTTGTA CAAAAAAGCAGGCTTAAACAATGATCAATCCACACGGTG 3′) and prm08181 (SEQ ID NO: 196; reverse, complementary, AttB2 site in italic: 5′ GGGGACCACTTTGTACAAGAAAG CTGGGTTCCTTGTTTACTCATTCCACA 3′), which include the AttB sites for Gateway recombination. The primers used to amplify SEQ ID NO: 177 (PLT2) were prm08182 (SEQ ID NO: 197; sense, start codon in bold, AttB1 site in italic: 5′GGGGACAAGTTTGTACAAAAAAGCAGGCTTAAACAATGAATTCTAACA ACTGGCTC 3′) and prm08183 (SEQ ID NO: 198; reverse, complementary, AttB2 site in italic: 5′ GGGGACCACTTTGTACAAGAAAGCTGGGTTCATCTTTTATTCATTCCACA 3′),

The amplified PCR fragments were purified also using standard methods. The first step of the Gateway procedure, the BP reaction, was then performed, during which the PCR fragment recombines in vivo with the pDONR201 plasmid to produce, according to the Gateway terminology, an “entry clone”, pPLT1 for SEQ ID NO: 175 and pPLT2 for SEQ ID NO: 177. Plasmid pDONR201 was purchased from Invitrogen, as part of the Gateway® technology.

Example 26 Expression Vector Construction

The entry clones pPLT1 and pPLT2 were subsequently used in an LR reaction with destination vectors used for Oryza sativa transformation. A first vector contains as functional elements within the T-DNA borders: a plant selectable marker; a screenable marker expression cassette; and a Gateway cassette intended for LR in vivo recombination with the nucleic acid sequence of interest already cloned in the entry clone. A rice constitutive promoter, a GOS2 promoter (SEQ ID NO: 210, alternatively SEQ ID NO: 194 is equally useful) was located upstream of this Gateway cassette.

A second vector contains the same functional elements within the T-DNA borders: a plant selectable marker; a screenable marker expression cassette; and a Gateway cassette intended for LR in vivo recombination with the nucleic acid sequence of interest already cloned in the entry clone. A rice promoter for expression in meristems, an MT promoter (SEQ ID NO: 211) (PRO0126) was located upstream of this Gateway cassette.

After the LR recombination step, the resulting expression vectors, pGOS2::PLT1, pGOS2; PLT2, pMT::PLT1 and pMT::PLT2 (FIG. 16 shows the construct with the GOS2 promoter) were independently transformed into Agrobacterium strain LBA4044 and subsequently to Oryza sativa plants. Transformed rice plants were allowed to grow and were then examined for the parameters described below.

Example 27 Crop Transformation

The transformed Agrobacterium icontaining the expression vectors were used independently to transform Oryza sativa plants. Mature dry seeds of the rice japonica cultivar Nipponbare were dehusked. Sterilization was carried out by incubating for one minute in 70% ethanol, followed by 30 minutes in 0.2% HgCl₂, followed by a 6 times 15 minutes wash with sterile distilled water. The sterile seeds were then germinated on a medium containing 2,4-D (callus induction medium). After incubation in the dark for four weeks, embryogenic, scutellum-derived calli were excised and propagated on the same medium. After two weeks, the calli were multiplied or propagated by subculture on the same medium for another 2 weeks. Embryogenic callus pieces were sub-cultured on fresh medium 3 days before co-cultivation (to boost cell division activity).

Agrobacterium strain LBA4404 containing the expression vector was used for co-cultivation. Agrobacterium was inoculated on AB medium with the appropriate antibiotics and cultured for 3 days at 28° C. The bacteria were then collected and suspended in liquid co-cultivation medium to a density (OD₆₀₀) of about 1. The suspension was then transferred to a Petri dish and the calli immersed in the suspension for 15 minutes. The callus tissues were then blotted dry on a filter paper and transferred to solidified, co-cultivation medium and incubated for 3 days in the dark at 25° C. Co-cultivated calli were grown on 2,4-D-containing medium for 4 weeks in the dark at 28° C. in the presence of a selection agent. During this period, rapidly growing resistant callus islands developed. After transfer of this material to a regeneration medium and incubation in the light, the embryogenic potential was released and shoots developed in the next four to five weeks. Shoots were excised from the calli and incubated for 2 to 3 weeks on an auxin-containing medium from which they were transferred to soil. Hardened shoots were grown under high humidity and short days in a greenhouse.

Approximately 35 independent T0 rice transformants were generated for one construct. The primary transformants were transferred from a tissue culture chamber to a greenhouse. After a quantitative PCR analysis to verify copy number of the T-DNA insert, only single copy transgenic plants that exhibit tolerance to the selection agent were kept for harvest of T1 seed. Seeds were then harvested three to five months after transplanting. The method yielded single locus transformants at a rate of over 50% (Aldemita and Hodges1996, Chan et al. 1993, Hiei et al. 1994).

Corn Transformation

Transformation of maize (Zea mays) is performed with a modification of the method described by Ishida et al. (1996) Nature Biotech 14(6): 745-50. Transformation is genotype-dependent in corn and only specific genotypes are amenable to transformation and regeneration. The inbred line A188 (University of Minnesota) or hybrids with A188 as a parent are good sources of donor material for transformation, but other genotypes can be used successfully as well. Ears are harvested from corn plant approximately 11 days after pollination (DAP) when the length of the immature embryo is about 1 to 1.2 mm. Immature embryos are cocultivated with Agrobacterium tumefaciens containing the expression vector, and transgenic plants are recovered through organogenesis. Excised embryos are grown on callus induction medium, then maize regeneration medium, containing the selection agent (for example imidazolinone but various selection markers can be used). The Petri plates are incubated in the light at 25° C. for 2-3 weeks, or until shoots develop. The green shoots are transferred from each embryo to maize rooting medium and incubated at 25° C. for 2-3 weeks, until roots develop. The rooted shoots are transplanted to soil in the greenhouse. T1 seeds are produced from plants that exhibit tolerance to the selection agent and that contain a single copy of the T-DNA insert.

Wheat Transformation

Transformation of wheat is performed with the method described by Ishida et al. (1996) Nature Biotech 14(6): 745-50. The cultivar Bobwhite (available from CIMMYT, Mexico) is commonly used in transformation. Immature embryos are co-cultivated with Agrobacterium tumefaciens containing the expression vector, and transgenic plants are recovered through organogenesis. After incubation with Agrobacterium, the embryos are grown in vitro on callus induction medium, then regeneration medium, containing the selection agent (for example imidazolinone but various selection markers can be used). The Petri plates are incubated in the light at 25° C. for 2-3 weeks, or until shoots develop. The green shoots are transferred from each embryo to rooting medium and incubated at 25° C. for 2-3 weeks, until roots develop. The rooted shoots are transplanted to soil in the greenhouse. T1 seeds are produced from plants that exhibit tolerance to the selection agent and that contain a single copy of the T-DNA insert.

Soybean Transformation

Soybean is transformed according to a modification of the method described in the Texas A&M U.S. Pat. No. 5,164,310. Several commercial soybean varieties are amenable to transformation by this method. The cultivar Jack (available from the Illinois Seed foundation) is commonly used for transformation. Soybean seeds are sterilised for in vitro sowing. The hypocotyl, the radicle and one cotyledon are excised from seven-day old young seedlings. The epicotyl and the remaining cotyledon are further grown to develop axillary nodes. These axillary nodes are excised and incubated with Agrobacterium tumefaciens containing the expression vector. After the cocultivation treatment, the explants are washed and transferred to selection media. Regenerated shoots are excised and placed on a shoot elongation medium. Shoots no longer than 1 cm are placed on rooting medium until roots develop. The rooted shoots are transplanted to soil in the greenhouse. T1 seeds are produced from plants that exhibit tolerance to the selection agent and that contain a single copy of the T-DNA insert.

Rapeseed/Canola Transformation

Cotyledonary petioles and hypocotyls of 5-6 day old young seedling are used as explants for tissue culture and transformed according to Babic et al. (1998, Plant Cell Rep 17: 183-188). The commercial cultivar Westar (Agriculture Canada) is the standard variety used for transformation, but other varieties can also be used. Canola seeds are surface-sterilized for in vitro sowing. The cotyledon petiole explants with the cotyledon attached are excised from the in vitro seedlings, and inoculated with Agrobacterium (containing the expression vector) by dipping the cut end of the petiole explant into the bacterial suspension. The explants are then cultured for 2 days on MSBAP-3 medium containing 3 mg/l BAP, 3% sucrose, 0.7% Phytagar at 23° C., 16 hr light. After two days of co-cultivation with Agrobacterium, the petiole explants are transferred to MSBAP-3 medium containing 3 mg/l BAP, cefotaxime, carbenicillin, or timentin (300 mg/l) for 7 days, and then cultured on MSBAP-3 medium with cefotaxime, carbenicillin, or timentin and selection agent until shoot regeneration. When the shoots are 5-10 mm in length, they are cut and transferred to shoot elongation medium (MSBAP-0.5, containing 0.5 mg/l BAP). Shoots of about 2 cm in length are transferred to the rooting medium (MS0) for root induction. The rooted shoots are transplanted to soil in the greenhouse. T1 seeds are produced from plants that exhibit tolerance to the selection agent and that contain a single copy of the T-DNA insert.

Alfalfa Transformation

A regenerating clone of alfalfa (Medicago sativa) is transformed using the method of (McKersie et al., 1999 Plant Physiol 119: 839-847). Regeneration and transformation of alfalfa is genotype dependent and therefore a regenerating plant is required. Methods to obtain regenerating plants have been described. For example, these can be selected from the cultivar Rangelander (Agriculture Canada) or any other commercial alfalfa variety as described by Brown D C W and A Atanassov (1985. Plant Cell Tissue Organ Culture 4: 111-112). Alternatively, the RA3 variety (University of Wisconsin) has been selected for use in tissue culture (Walker et al., 1978 Am J Bot 65:654-659). Petiole explants are cocultivated with an overnight culture of Agrobacterium tumefaciens C58C1 pMP90 (McKersie et al., 1999 Plant Physiol 119: 839-847) or LBA4404 containing the expression vector. The explants are cocultivated for 3 d in the dark on SH induction medium containing 288 mg/L Pro, 53 mg/L thioproline, 4.35 g/L K₂SO₄, and 100 μm acetosyringinone. The explants are washed in half-strength Murashige-Skoog medium (Murashige and Skoog, 1962) and plated on the same SH induction medium without acetosyringinone but with a suitable selection agent and suitable antibiotic to inhibit Agrobacterium growth. After several weeks, somatic embryos are transferred to BOi2Y development medium containing no growth regulators, no antibiotics, and 50 g/L sucrose. Somatic embryos are subsequently germinated on half-strength Murashige-Skoog medium. Rooted seedlings were transplanted into pots and grown in a greenhouse. T1 seeds are produced from plants that exhibit tolerance to the selection agent and that contain a single copy of the T-DNA insert.

Example 28 Phenotypic Evaluation Procedure 28.1 Evaluation Setup Evaluation in Normal Growth Conditions

The primary transformants were transferred from a tissue culture chamber to a greenhouse for growing and harvest of T1 seed. Six events, of which the T1 progeny segregated 3:1 for presence/absence of the transgene, were retained. For each of these events, approximately 10 T1 seedlings containing the transgene (hetero- and homo-zygotes) and approximately 10 T1 seedlings lacking the transgene (nullizygotes) were selected by monitoring visual marker expression. The transgenic plants and the corresponding nullizygotes were grown side-by-side at random positions. Greenhouse conditions were of shorts days (12 hours light), 28° C. in the light and 22° C. in the dark, and a relative humidity of 70%.

Evaluation Under Reduced Nitrogen Availability

The rice plants were grown in potting soil as under normal conditions except for the nutrient solution. The pots were watered from transplantation to maturation with a specific nutrient solution containing reduced N nitrogen (N) content, usually between 7 to 8 times less. The rest of the cultivation (plant maturation, seed harvest) was the same as for plants not grown under abiotic stress.

28.2 Statistical Analysis: F-Test

A two factor ANOVA (analysis of variants) was used as a statistical model for the overall evaluation of plant phenotypic characteristics. An F-test was carried out on all the parameters measured of all the plants of all the events transformed with the gene of the present invention. The F-test was carried out to check for an effect of the gene over all the transformation events and to verify for an overall effect of the gene, also known as a global gene effect. The threshold for significance for a true global gene effect was set at a 5% probability level for the F-test. A significant F-test value points to a gene effect, meaning that it is not only the mere presence or position of the gene that is causing the differences in phenotype.

To check for an effect of the genes within an event, i.e., for a line-specific effect, a t-test was performed within each event using data sets from the transgenic plants and the corresponding null plants. “Null plants” or “null segregants” or “nullizygotes” are the plants treated in the same way as the transgenic plant, but from which the transgene has segregated. Null plants can also be described as the homozygous negative transformed plants. The threshold for significance for the t-test is set at 10% probability level. The results for some events can be above or below this threshold. This is based on the hypothesis that a gene might only have an effect in certain positions in the genome, and that the occurrence of this position-dependent effect is not uncommon. This kind of gene effect is also named herein a “line effect of the gene”. The p-value is obtained by comparing the t-value to the t-distribution or alternatively, by comparing the F-value to the F-distribution. The p-value then gives the probability that the null hypothesis (i.e., that there is no effect of the transgene) is correct.

28.3 Parameters Measured

Biomass-Related Parameter Measurement From the stage of sowing until the stage of maturity the plants were passed several times through a digital imaging cabinet. At each time point digital images (2048×1536 pixels, 16 million colours) were taken of each plant from at least 6 different angles.

The plant aboveground area (or leafy biomass, areamax) was determined by counting the total number of pixels on the digital images from aboveground plant parts discriminated from the background. This value was averaged for the pictures taken on the same time point from the different angles and was converted to a physical surface value expressed in square mm by calibration. Experiments show that the aboveground plant area measured this way correlates with the biomass of plant parts above ground. The above ground area is the area measured at the time point at which the plant had reached its maximal leafy biomass. The early vigour is the plant (seedling) aboveground area three weeks post-germination. Increase in root biomass is expressed as an increase in total root biomass (measured as maximum biomass of roots observed during the lifespan of a plant); or as an increase in the root/shoot index (measured as the ratio between root mass and shoot mass in the period of active growth of root and shoot).

Seed-Related Parameter Measurements

The mature primary panicles were harvested, counted, bagged, barcode-labelled and then dried for three days in an oven at 37° C. The panicles were then threshed and all the seeds were collected and counted. The filled husks were separated from the empty ones using an air-blowing device. The empty husks were discarded and the remaining fraction was counted again. The filled husks were weighed on an analytical balance. The number of filled seeds was determined by counting the number of filled husks that remained after the separation step. The total seed yield was measured by weighing all filled husks harvested from a plant. Total seed number per plant was measured by counting the number of husks harvested from a plant. Thousand Kernel Weight (TKW) is extrapolated from the number of filled seeds counted and their total weight. The Harvest Index (HI) in the present invention is defined as the ratio between the total seed yield and the above ground area (mm²), multiplied by a factor 10⁶. The total number of flowers per panicle as defined in the present invention is the ratio between the total number of seeds and the number of mature primary panicles. The seed fill rate as defined in the present invention is the proportion (expressed as a %) of the number of filled seeds over the total number of seeds (or florets).

Example 29 Results of the Phenotypic Evaluation of the Transgenic Plants 29.1 Results of the Phenotypic Evaluation of the Transgenics Plants Grown Under Normal Growth Conditions, Expressing Either PLT1 or PLT2 Nucleic Acid Sequence Under the Control of a Constitutive Promoter

The TKW measurement results of the T1 seeds of PLT1 and PLT2 transgenic rice plants grown under normal growth conditions, are shown in Table J, in absolute values (averaged events) and as a percentage compard to wild type plants. A substantial increase in TKW is observed for the transgenic seeds containing either construct, compared to wild type seeds.

TABLE J Results of TKW measurements of the T1 seeds of PLT1 and PLT2 transgenic plants grown under normal growth conditions. TKW (g) % increase PLT1 transgenics 0.0290 16% PLT2 transgenics 0.0288 15% WT 0.0250

Individual seed parameters (including width, length, area, weight) were measured using a custom-made device consisting of two main components, a weighing and imaging device, coupled to software for image analysis.

The seed area and seed length measurement results of T1 seeds of PLT1 and PLT2 transgenic rice plants are shown in Table K in absolute values (averaged events) and as a percentage compard to wild type plants. A clear increase in both seed area and seed length is observed for the transgenic seeds containing either construct, compared to wild type seeds.

TABLE K Results of seed area and seed length measurements of the T1 seeds of PLT1 and PLT2 transgenic plants grown under normal growth conditions. Seed area (mm²) % increase Seed length (mm) % increase PLT1 transgenics 27.60 12% 9.4 13% PLT2 transgenics 27.35 11% 9.4 13% WT 24.56 8.3

Seed width was not significantly affected on the T1 seeds of the PLT and PLT2 transgenic plants (data not shown).

29.2 Results of the Phenotypic Evaluation of the Transgenics Plants Grown Under Reduced Nitrogen Availability Conditions, Expressing Either PLT1 or PLT2 Nucleic Acid Sequence Under the Control of a Constitutive Promoter

The TKW measurement results of the T1 seeds of PLT1 and PLT2 transgenic rice plants grown under reduced nitrogen availability conditions, are shown in Table L, in absolute values (averaged events) and as a percentage compard to wild type plants. A substantial increase in TKW is observed for the transgenic seeds containing either construct, compared to wild type seeds.

TABLE L Results of TKW measurements of the T1 seeds of PLT1 and PLT2 transgenic plants grown under reduced nitrogen availability conditions. TKW (g) % increase PLT1 transgenics 0.0295 12% PLT2 transgenics 0.0278 8% WT 0.0256

29.3 Results of the Phenotypic Evaluation of the Transqenics Plants Grown Under Normal Growth Conditions, Expressing PLT2 Nucleic Acid Sequence Under the Control of a Meristem-Specific Promoter

The TKW measurement results of the T1 seeds PLT2 transgenic rice plants grown under normal growth conditions, expressing PLT2 nucleic acid sequence under the control of a meristem-specific promoter, are shown in Table M, in absolute values (averaged events) and as a percentage compard to wild type plants. A substantial increase in TKW is observed for the transgenic seeds containing the construct, compared to wild type seeds.

TABLE M Results of TKW measurements of the T1 seeds of PLT2 transgenic plants grown under normal growth conditions, expressing PLT2 nucleic acid sequence under the control of a mersitem-specific promoter. TKW (g) % increase PLT2 transgenics 0.0263 3% WT 0.0254

Example Section E bHLH Example 30 Identification of Paralogues of the bHLH of SEQ ID NO: 213 in Rice

SEQ ID 2 was used to search for paralogues in the rice genome using a BLASTP algorithm used to perform similarity searches of a protein query sequence to a given database of protein sequences. The protein database queried corresponded to the rice proteome of the MIPS institute, the MIPS Oryza sativa Database (MOsDB), comprising 59,712 sequences; 27,051,637 total letters. Results were ranked according to highest similarity as determined from highest score and lowest e-value. Hits identifying bHLH protein sequences paralogous to SEQ ID NO: 2 had a score of at least 50 and an e-value lower than e-05. Pairwise alignments between the query sequence and the de novo identified paralogues are shown below.

Query: SEQID 2 Smallest Sum High Probability Sequences producing High-scoring Segment Pairs: Score P(N) N 9629.m00093|protein Helix-loop-helix DNA-binding domain, . . .  1132  1.3e-115 1 9629.m00090|protein Helix-loop-helix DNA-binding domain, . . .  305 5.7e-28 1 9630.m01262|protein Helix-loop-helix DNA-binding domain, . . .  189 1.1e-15 1 9629.m07159|protein Helix-loop-helix DNA-binding domain, . . .  112 3.4e-05 1 >9629.m00093|protein Helix-loop-helix DNA-binding domain, putative Length = 225 Score = 1132 (403.5 bits), Expect = 1.3e-115, P = 1.3e-115 Identities = 224/224 (100%), Positives = 224/224 (100%) Query:   1 MKSRKNSTTSTKAAGSCHTSSSGGGGGGGNCYSSSSSKMERKDVEKNRRLHMKGLCLKLS 60     MKSRKNSTTSTKAAGSCHTSSSGGGGGGGNCYSSSSSKMERKDVEKNRRLHMKGLCLKLS Sbjct:   1 MKSRKNSTTSTKAAGSCHTSSSGGGGGGGNCYSSSSSKMERKDVEKNRRLHMKGLCLKLS 60 Query:  61 SLIPAAAPRRHHHHYSTSSSSSPPSSTKEAVTQLDHLEQAAAYIKQLKGRIDELKKRKQQ 120     SLIPAAAPRRHHHHYSTSSSSSPPSSTKEAVTQLDHLEQAAAYIKQLKGRIDELKKRKQQ Sbjct:  61 SLIPAAAPRRHHHHYSTSSSSSPPSSTKEAVTQLDHLEQAAAYIKQLKGRIDELKKRKQQ 120 Query: 121 AAALTTSTSNGGGGGMPVVEVRCQDGTLDVVVVSEAIREERERAVRLHEVIGVLEEEGAE 180     AAALTTSTSNGGGGGMPVVEVRCQDGTLDVVVVSEAIREERERAVRLHEVIGVLEEEGAE Sbjct: 121 AAALTTSTSNGGGGGMPVVEVRCQDGTLDVVVVSEAIREERERAVRLHEVIGVLEEEGAE 180 Query: 181 VVNASFSVVGDKIFYTLHSQALCSRIGLDASRVSHRLRNLLLQY 224     VVNASFSVVGDKIFYTLHSQALCSRIGLDASRVSHRLRNLLLQY Sbjct: 181 VVNASFSVVGDKIFYTLHSQALCSRIGLDASRVSHRLRNLLLQY 224 >9629.m00090|protein Helix-loop-helix DNA-binding domain, putative Length = 363 Score = 305 (112.4 bits), Expect = 5.7e-28, P = 5.7e-28 Identities = 87/230 (37%), Positives = 126/230 (54%) Query:  19 TSSSGGGGGGGNCYSSSSSKMERKDVEKNRRLHMKGLCLKLSSLIPAAAPRRHHHHYSTS 78     TSSSG G       +++++  ERK++E+ RR  MKGLC+KL+SLIP     + H   S Sbjct:  18 TSSSGSGASS----TAAAAAAERKEMERRRRQDMKGLCVKLASLIP-----KEHCSMSKM 68 Query:  79 SSSSPPSSTKEAVTQLDHLEQAAAYIKQLKGRIDELKKRKQQ----------------AA 122      ++S         TQL  L++AAAYIK+LK R+DEL  ++                  AA Sbjct:  69 QAASR--------TQLGSLDEAAAYIKKLKERVDELHHKRSMMSITSSRCRSGGGGGPAA 120 Query: 123 ALTTSTSNGGGGGMPVVEVRCQDGTLDVVVVSEAIRE------------ERERAVRLHEV 170     A   STS GGGG     ++        VV V + ++E               R V+ H+V Sbjct: 121 AAGQSTSGGGGGEEEEEDMTRTTAAAAVVEVRQHVQEGSLISLDVVLICSAARPVKFHDV 180 Query: 171 IGVLEEEGAEVVNASFSVVGDKIFYTLHSQALCSRIGLDASRVSHRLRNL 220     I VLEEEGA++++A+FS+     +YT++S+A  SRIG++ASR+S RLR L Sbjct: 181 ITVLEEEGADIISANFSLAAHNFYYTIYSRAFSSRIGIEASRISERLRAL 230 >9630.m01262|protein Helix-loop-helix DNA-binding domain, putative Length = 211 Score = 189 (71.6 bits), Expect = 1.1e-15, P = 1.1e-15 Identities = 66/214 (30%), Positives = 102/214 (47%) Query:  21 SSGGGGGGGNCYSSSSSKMERKDVEKNRRLHMKGLCLKLSSLIPAAAPRRHH-HHYSTSS 79     S+GGGGGGG        K +RK  E+ RR  M  L   L SL+ +A P  +    +S S+ Sbjct:   7 SAGGGGGGG--------KPDRKTTERIRREQMNKLYSHLDSLVRSAPPTVNSIPSHSNSN 58 Query:  80 SSSPPSSTK------EAVTQLDHLEQAAAYIKQLKGRIDELKKRKQQ---AAALTTSTSN 130     S       +       A T+ D L  AA YI+Q + R+D L+++K++       +S+S+ Sbjct:  59 SKYHQRKLRILGGAAAATTRPDRLGVAAEYIRQTQERVDMLREKKRELTGGGGGGSSSSS 118 Query: 131 GGGGGM---PVVEVRCQDGTLDVVVVSEAIREERERAVRLHEVIGVLEEEGAEVVNASFS 187     G G      P VEV+     L  ++ + A   +       H  +  +E+ G +V NA FS Sbjct: 119 GAGAATAAAPEVEVQHLGSGLHAILFTGAPPTD---GASFHRAVRAVEDAGGQVQNAHFS 175 Query: 188 VVGDKIFYTLHSQALCSRIGLDASRVSHRLRNLL 221     V G K  YT+H+       G++  RV  RL+  + Sbjct: 176 VAGAKAVYTIHAMIGDGYGGIE--RVVQRLKEAI 207

Example 31 Identification of Orthologues of the bHLH of SEQ ID NO: 213 in Arabidopsis thaliana

SEQ ID 2 was used to search for orthologues in the Arabidopsis genome using a BLASTP algorithm used to perform a similarity search of a protein query sequence to a given database of protein sequences. The protein database queried corresponded to the Arabidopsis proteome of the MIPS institute, the MIPS Arabidopsis thaliana database (MAtDB) comprising 26,735 sequences; 11,317,104 total letters. Results were ranked according to highest similarity as determined from highest score and lowest e-value. Hits identifying bHLH protein sequences orthologous to SEQ ID2 had a score of at least 50 and an e-value lower than e-05. Pairwise alignments between the query sequence and the de novo identified orthologue are shown below.

Query: SEQID 2 Database: /home/data/blast/orgs_sets/arabi 26,735 sequences; 11,317,104 total letters. Smallest Sum High Probability Sequences producing High-scoring Segment Pairs: Score P(N) N At1g10585 unknown protein 180 4.5e-15 1 At4g20970 hypothetical protein 149 8.7e-12 1 At4g25410 putative protein 118 2.0e-06 1 At5g51780 putative bHLH transcription factor (bHLH036) 105 1.5e-05 1 At5g51790 putative protein 110 1.5e-05 1 >At1g10585 unknown protein Length = 122 Score = 180 (68.4 bits), Expect = 4.5e-15, P = 4.5e-15 Identities = 38/119 (31%), Positives = 72/119 (60%) Query: 106 QLKGRIDELKKRKQQAAALTTSTSNGGGGGMPVVEVRCQDGTLDVVVVSEAIREERERAV 165     QLK  ++ LK++K+            G   +P + +R +D T+++ ++ + +  +R   V Sbjct:   3 QLKENVNYLKEKKRTLLQGELGNLYEGSFLLPKLSIRSRDSTIEMNLIMD-LNMKR---V 58 Query: 166 RLHEVIGVLEEEGAEVVNASFSVVGDKIFYTLHSQALCSRIGLDASRVSHRLRNLLLQY 224      LHE++ + EEEGA+V++A+   + D+  YT+ +QA+ SRIG+D SR+  R+R ++  Y Sbjct:  59 MLHELVSIFEEEGAQVMSANLQNLNDRTTYTIIAQAIISRIGIDPSRIEERVRKIIYGY 117 >At4g20970 hypothetical protein Length = 167 Score = 149 (57.5 bits), Expect = 8.7e-12, P = 8.7e-12 Identities = 49/171 (28%), Positives = 86/171 (50%) Query:  33 SSSSSKMERKDVEKNRRLHMKGLCLKLSSLIPAAAPRRHHHHYSTSSSSSPPSSTKEAVT 92     +  S  ++RK VEKNRR+ MK L  +L SL+P        HH ST   + P     EA Sbjct:   8 TGQSRSVDRKTVEKNRRMQMKSLYSELISLLP--------HHSSTEPLTLP-DQLDEAAN 58 Query:  93 QLDHLEQAAAYIKQLKGRI---DELKKRKQQ-AAALTTSTSNGGGGGMPVVEVRCQDGTL 148      +  L+      ++ K  +     L+K     ++++++S        +P +E++ + G++ Sbjct:  59 YIKKLQVNVEKKRERKRNLVATTTLEKLNSVGSSSVSSSVDVSVPRKLPKIEIQ-ETGSI 117 Query: 149 DVVVVSEAIREERERAVRLHEVIGVLEEE-GAEVVNASFSVVGDKIFYTLH 198       + +  ++    E      E+I VL EE GAE+ +A +S+V D +F+TLH Sbjct: 118 FHIFLVTSL----EHKFMFCEIIRVLTEELGAEITHAGYSIVDDAVFHTLH 164

Example 32 Identification of a bHLH from Medicago truncatula

The question to be addressed was whether the query sequence (SEQ ID NO: 227 from Medicago truncatula) was a bHLH polypeptide according to the definition applied herein. SEQ ID 227 was compared to the Arabidopsis proteome database of the MIPS institute.

Comparison was carried out using the BLASTP 2.0 MP-WashU algorithm, which performs similarity searches of a protein query sequence to a given database of protein sequences. (Reference: Gish, W. (1996-2002)). The parameters used in the comparison were E value 10 Cutoff score (S2): 56

The protein database queried corresponded to the Arabidopsis proteome of the MIPS institute comprising 26,735 sequences (Database: /home/data/blast/orgs_sets/arabi 26,735 sequences; 11,317,104 total letters). Results were ranked according to highest similarity as determined from highest score and lowest e-value. The first Hit identified (underlined in the alignment) corresponded to SEQ ID NO: 225 (At4g20970) indicating that the sequence is a bHLH polypeptide according to the definition applied herein. Pairwise alignments between the query sequence from Medicago and the first hit corresponding to the de novo identified bHLH are shown below.

BLASTP 2.0 MP-WashU [9 Sep. 2002] [decunix4.0-ev56-132LPF64 2002-09-09T17:45:09]

Query = SEQ ID NO: 227 (140 letters) Database: /home/data/blast/orgs_sets/arabi 26,735 sequences; 11,317,104 total letters. Searching . . . 10 . . . 20 . . . 30 . . . 40 . . . 50 . . . 60 . . . 70 . . .  80 . . . 90 . . . 100% done Smallest Sum High Probability Sequences producing High-scoring Segment Pairs: Score P(N) N At4g20970 hypothetical protein 248 2.8e-22 1 At5g51780 putative bHLH transcription factor (bHLH036) 103 6.5e-07 1 At1g10585 unknown protein 100 1.4e-06 1 At4g25400 putative bHLH transcription factor (bHLH118) 99 7.3e-06 1 >At4g20970 hypothetical protein Length = 167 Score = 248 (92.4 bits), Expect = 2.8e-22, P = 2.8e-22 Identities = 52/123 (42%), Positives = 82/123 (66%) Query:   7 EAISVPDQLKEATNYIKKLQINLEKMKEKKNFLLG---IQRPN------VNLNRNQKMGL 57     E +++PDQL EA NYIKKLQ+N+EK +E+K  L+    +++ N      V+ + + + Sbjct:  45 EPLTLPDQLDEAANYIKKLQVNVEKKRERKRNLVATTTLEKLNSVGSSSVSSSVDVSVPR 104 Query:  58 KSPKIKIQQIGLVLEVVLITGLESQFLFSETFRVLHEE-GVDIVNASYKVNEDSVFHSIH 116     K PKI+IQ+ G +  + L+T LE +F+F E  RVL EE G +I +A Y + +D+VFH++H Sbjct: 105 KLPKIEIQETGSIFHIFLVTSLEHKFMFCEIIRVLTEELGAEITHAGYSIVDDAVFHTLH 164 Query: 117 CQV 119     C+V Sbjct: 165 CKV 167

Example 33 Identification of Sequences Related to the Nucleic Acid Sequence Used in the Methods of the Invention

bHLH Sequences, whether nucleotide (full length cDNA, ESTs or genomic) or protein (full length or partial polypeptides), were used to identified other bHLH nucleotide or proteins sequences amongst those maintained in the Entrez Nucleotides database at the National Center for Biotechnology Information (NCBI) using database sequence search tools, such as the Basic Local Alignment Tool (BLAST) (Altschul et al. (1990) J. Mol. Biol. 215:403-410; and Altschul et al. (1997) Nucleic Acids Res. 25:3389-3402). The program was used to find regions of local similarity between sequences by comparing nucleic acid or polypeptide sequences to sequence databases and by calculating the statistical significance of matches. For example, the polypeptide encoded by SEQ ID NO: 213 was used as query to the nr (non-redundant: (Database: All GenBank+EMBL+DDBJ+PDB sequences (but no EST, STS, GSS,environmental samples or phase 0, 1 or 2 HTGS sequences) 3,819,973 sequences; 16,928,533,343 total letters) database sequence using the TBLASTN algorithm, with default settings and the filter to ignore low complexity sequences. The output of the analysis (shown below) was viewed by pairwise comparison, and ranked according to the probability score (E-value), where the score reflect the probability that a particular alignment occurs by chance (the lower the E-value, the more significant the hit). In addition to E-values, comparisons were also scored by percentage identity. Percentage identity refers to the number of identical nucleotides (or amino acids) between the two compared nucleic acid (or polypeptide) sequences over a particular length.

Hits on the database identifying BHLH proteins produced a score of at least 50 and an e-value equal to or lower than e-05.

Score E Sequences producing significant alignments: (Bits) Value gi|55765745|ref|NM_183508.2|Oryza sativa (japonica cultivar-gro 440 1e−121 gi|42821746|dbj|AK109432.2|Oryza sativa (japonica cultivar-g... 440 1e−121 gi|55769744|ref|XM_549862.1|Oryza sativa (japonica cultivar-gro 247 1e−105 gi|58530787|dbj|AP008207.1|Oryza sativa (japonica cultivar-g... 263 2e−68 gi|17385651|dbj|AP002845.3|Oryza sativa (japonica cultivar-g... 263 2e−68 gi|32980356|dbj|AK070332.1|Oryza sativa (japonica cultivar-g... 251 9e−65 gi|34894135|ref|NM_183504.1|Oryza sativa (japonica cultivar-gro 137 3e−30 gi|15293050|gb|AY050959.1|Arabidopsis thaliana unknown prote... 80.1 6e−16 gi|79340923|ref|NM_100934.2|Arabidopsis thaliana transcripti... 87.8 2e−15 gi|58531195|dbj|AP008214.1|Oryza sativa (japonica cultivar-g... 51.6 4e−13 gi|42408246|dbj|AP004557.3|Oryza sativa (japonica cultivar-g... 51.6 4e−13 gi|42408168|dbj|AP004376.3|Oryza sativa (japonica cultivar-g... 51.6 4e−13 gi|22328837|ref|NM_118215.2|Arabidopsis thaliana DNA binding... 78.2 1e−12 gi|7268888|emb|AL161554.2|ATCHRIV54 Arabidopsis thaliana DNA chr 77.8 2e−12 gi|5262774|emb|AL080282.1|ATT13K14 Arabidopsis thaliana DNA c... 77.8 2e−12 gi|50906596|ref|XM_464787.1|Oryza sativa (japonica cultivar-gro 77.0 3e−12

Example 34 Determination of Global Similarity and Identity Between bHLH Transcription Factors

Global percentages similarity and identity between bHLH polypeptides was determined using the MatGAT software (BMC Bioinformatics. 2003 Jul. 10; 4:29. MatGAT: an application that generates similarity/identity matrices using protein or DNA sequences. Campanella J J, Bitincka L, Smalley J.). MatGAT software generates similarity/identity matrices for DNA or protein sequences without needing pre-alignment of the data. The program performs a series of pair-wise alignments, calculates similarity and identity, and then places the results in a distance matrix.

Parameters used in the comparison were:

-   -   Scoring matrix: Blosum62     -   First Gap: 12     -   Extending gap: 2

Results are shown in FIG. 19 a.

Example 35 Determination of Global Similarity and Identity Between bHLH Domains in bHLH Polypeptides

bHLH domains were mapped using the SMART software (Schultz et al. (1998) Proc. Natl. Acad. Sci. USA 95, 5857-5864; Letunic et al. (2006) Nucleic Acids Res 34, D257-D260). Smart software is available through EMBL institute(European Molecular Biology Laboratory (EMBL).

The sequences of the bHLH domain used are given below.

Hv_BHLH KESEKERRKRMKALCEKLASLIPREHCCSTTDTMTQLGSLDVGASYIKKL KERVDE OS_NP_908393_BHLH KEMERRRRQDMKGLCVKLASLIPKEHCSMSKMQAASRTQLGSLDEAAAYI KKLKERVDE OS_NP_908397.1_BHLH KDVEKNRRLHMKGLCLKLSSLIPAAAPRRHHHHYSTSSSSSPPSSTKEAV TQLDHLEQAAAYIKQLKGRIDE Os_XP_464787.1_BHLH KTTERIRREQMNKLYSHLDSLVRSAPPTVNSIPSHSNSNSKYHQRKLRIL GGAAAATTRPDRLGVAAEYIRQTQERVDM AT1G10585_bHLH nlrekdrrmrmkhlfsilsshvsptrklpvphlidqatsymiqlkenvny At4g20970_bHLH KTVEKNRRMQMKSLYSELISLLPHHSSTEPLTLPDQLDEAANYIKKLQVN VEK

Global percentages of similarity and identity between bHLH domains of bHLH polypeptides were determined using the software and parameters described in Example 34.

Results are shown in FIG. 19 b.

Example 36 Cloning of the Nucleic Acid Sequence Used in the Methods of the Invention

The nucleic acid sequence used in the methods of the invention was amplified by PCR using as template a custom-made Oryza sativa seedlings cDNA library (in pCMV Sport 6.0; Invitrogen, Paisley, UK). PCR was performed using Hifi Taq DNA polymerase in standard conditions, using 200 ng of template in a 50 μl PCR mix. The primers used were prm06808 (SEQ ID NO: 231; sense, start codon in bold, AttB1 site in italic: 5′-ggggacaagtttgtacaaaaaagcaggcttaaacaatgaagagcaggaagaacagc 3′) and prm06809 (SEQ ID NO: 232; reverse, complementary, AttB2 site in italic: 5′ ggggaccactttgtacaagaaagctgggtgcagagtgaaagagtggtgtg 3′), which include the AttB sites for Gateway recombination. The amplified PCR fragment was purified also using standard methods. The first step of the Gateway procedure, the BP reaction, was then performed, during which the PCR fragment recombines in vivo with the pDONR201 plasmid to produce, according to the Gateway terminology, an “entry clone”, pbHLH. Plasmid pDONR201 was purchased from Invitrogen, as part of the Gateway® technology.

Example 37 Expression Vector Construction

The entry clone p076 was subsequently used in an LR reaction with pGOS2, a destination vector used for Oryza sativa transformation. This vector contains as functional elements within the T-DNA borders: a plant selectable marker; a screenable marker expression cassette; and a Gateway cassette intended for LR in vivo recombination with the nucleic acid sequence of interest already cloned in the entry clone. A rice GOS2 promoter (SEQ ID NO: 233, alternatively, SEQ ID NO: 230 is equally useful) for constitutive expression (internal reference PRO0129) was located upstream of this Gateway cassette.

After the LR recombination step, the resulting expression vector pGOS2::bHLH (FIG. 20) was transformed into Agrobacterium strain LBA4044 and subsequently to Oryza sativa plants.

Example 38 Plant Transformation Rice Transformation

The Agrobacterium containing the expression vector was used to transform Oryza sativa plants. Mature dry seeds of the rice japonica cultivar Nipponbare were dehusked. Sterilization was carried out by incubating for one minute in 70% ethanol, followed by 30 minutes in 0.2% HgCl₂, followed by a 6 times 15 minutes wash with sterile distilled water. The sterile seeds were then germinated on a medium containing 2,4-D (callus induction medium). After incubation in the dark for four weeks, embryogenic, scutellum-derived calli were excised and propagated on the same medium. After two weeks, the calli were multiplied or propagated by subculture on the same medium for another 2 weeks. Embryogenic callus pieces were sub-cultured on fresh medium 3 days before co-cultivation (to boost cell division activity).

Agrobacterium strain LBA4404 containing the expression vector was used for co-cultivation. Agrobacterium was inoculated on AB medium with the appropriate antibiotics and cultured for 3 days at 28° C. The bacteria were then collected and suspended in liquid co-cultivation medium to a density (OD₆₀₀) of about 1. The suspension was then transferred to a Petri dish and the calli immersed in the suspension for 15 minutes. The callus tissues were then blotted dry on a filter paper and transferred to solidified, co-cultivation medium and incubated for 3 days in the dark at 25° C. Co-cultivated calli were grown on 2,4-D-containing medium for 4 weeks in the dark at 28° C. in the presence of a selection agent. During this period, rapidly growing resistant callus islands developed. After transfer of this material to a regeneration medium and incubation in the light, the embryogenic potential was released and shoots developed in the next four to five weeks. Shoots were excised from the calli and incubated for 2 to 3 weeks on an auxin-containing medium from which they were transferred to soil. Hardened shoots were grown under high humidity and short days in a greenhouse.

Approximately 30 independent T0 rice transformants were generated for one construct. The primary transformants were transferred from a tissue culture chamber to a greenhouse. After a quantitative PCR analysis to verify copy number of the T-DNA insert, only single copy transgenic plants that exhibit tolerance to the selection agent were kept for harvest of T1 seed. Seeds were then harvested three to five months after transplanting. The method yielded single locus transformants at a rate of over 50% (Aldemita and Hodges1996, Chan et al. 1993, Hiei et al. 1994).

Corn Transformation

Transformation of maize (Zea mays) is performed with a modification of the method described by Ishida et al. (1996) Nature Biotech 14(6): 745-50. Transformation is genotype-dependent in corn and only specific genotypes are amenable to transformation and regeneration. The inbred line A188 (University of Minnesota) or hybrids with A188 as a parent are good sources of donor material for transformation, but other genotypes can be used successfully as well. Ears are harvested from corn plant approximately 11 days after pollination (DAP) when the length of the immature embryo is about 1 to 1.2 mm. Immature embryos are cocultivated with Agrobacterium tumefaciens containing the expression vector, and transgenic plants are recovered through organogenesis. Excised embryos are grown on callus induction medium, then maize regeneration medium, containing the selection agent (for example imidazolinone but various selection markers can be used). The Petri plates are incubated in the light at 25° C. for 2-3 weeks, or until shoots develop. The green shoots are transferred from each embryo to maize rooting medium and incubated at 25° C. for 2-3 weeks, until roots develop. The rooted shoots are transplanted to soil in the greenhouse. T1 seeds are produced from plants that exhibit tolerance to the selection agent and that contain a single copy of the T-DNA insert.

Wheat Transformation

Transformation of wheat is performed with the method described by Ishida et al. (1996) Nature Biotech 14(6): 745-50. The cultivar Bobwhite (available from CIMMYT, Mexico) is commonly used in transformation. Immature embryos are co-cultivated with Agrobacterium tumefaciens containing the expression vector, and transgenic plants are recovered through organogenesis. After incubation with Agrobacterium, the embryos are grown in vitro on callus induction medium, then regeneration medium, containing the selection agent (for example imidazolinone but various selection markers can be used). The Petri plates are incubated in the light at 25° C. for 2-3 weeks, or until shoots develop. The green shoots are transferred from each embryo to rooting medium and incubated at 25° C. for 2-3 weeks, until roots develop. The rooted shoots are transplanted to soil in the greenhouse. T1 seeds are produced from plants that exhibit tolerance to the selection agent and that contain a single copy of the T-DNA insert.

Soybean Transformation

Soybean is transformed according to a modification of the method described in the Texas A&M U.S. Pat. No. 5,164,310. Several commercial soybean varieties are amenable to transformation by this method. The cultivar Jack (available from the Illinois Seed foundation) is commonly used for transformation. Soybean seeds are sterilised for in vitro sowing. The hypocotyl, the radicle and one cotyledon are excised from seven-day old young seedlings. The epicotyl and the remaining cotyledon are further grown to develop axillary nodes. These axillary nodes are excised and incubated with Agrobacterium tumefaciens containing the expression vector. After the cocultivation treatment, the explants are washed and transferred to selection media. Regenerated shoots are excised and placed on a shoot elongation medium. Shoots no longer than 1 cm are placed on rooting medium until roots develop. The rooted shoots are transplanted to soil in the greenhouse. T1 seeds are produced from plants that exhibit tolerance to the selection agent and that contain a single copy of the T-DNA insert.

Rapeseed/Canola Transformation

Cotyledonary petioles and hypocotyls of 5-6 day old young seedling are used as explants for tissue culture and transformed according to Babic et al. (1998, Plant Cell Rep 17: 183-188). The commercial cultivar Westar (Agriculture Canada) is the standard variety used for transformation, but other varieties can also be used. Canola seeds are surface-sterilized for in vitro sowing. The cotyledon petiole explants with the cotyledon attached are excised from the in vitro seedlings, and inoculated with Agrobacterium (containing the expression vector) by dipping the cut end of the petiole explant into the bacterial suspension. The explants are then cultured for 2 days on MSBAP-3 medium containing 3 mg/l BAP, 3% sucrose, 0.7% Phytagar at 23° C., 16 hr light. After two days of co-cultivation with Agrobacterium, the petiole explants are transferred to MSBAP-3 medium containing 3 mg/l BAP, cefotaxime, carbenicillin, or timentin (300 mg/l) for 7 days, and then cultured on MSBAP-3 medium with cefotaxime, carbenicillin, or timentin and selection agent until shoot regeneration. When the shoots are 5-10 mm in length, they are cut and transferred to shoot elongation medium (MSBAP-0.5, containing 0.5 mg/l BAP). Shoots of about 2 cm in length are transferred to the rooting medium (MS0) for root induction. The rooted shoots are transplanted to soil in the greenhouse. T1 seeds are produced from plants that exhibit tolerance to the selection agent and that contain a single copy of the T-DNA insert.

Alfalfa Transformation

A regenerating clone of alfalfa (Medicago sativa) is transformed using the method of (McKersie et al., 1999 Plant Physiol 119: 839-847). Regeneration and transformation of alfalfa is genotype dependent and therefore a regenerating plant is required. Methods to obtain regenerating plants have been described. For example, these can be selected from the cultivar Rangelander (Agriculture Canada) or any other commercial alfalfa variety as described by Brown D C W and A Atanassov (1985. Plant Cell Tissue Organ Culture 4: 111-112). Alternatively, the RA3 variety (University of Wisconsin) has been selected for use in tissue culture (Walker et al., 1978 Am J Bot 65:654-659). Petiole explants are cocultivated with an overnight culture of Agrobacterium tumefaciens C58C1 pMP90 (McKersie et al., 1999 Plant Physiol 119: 839-847) or LBA4404 containing the expression vector. The explants are cocultivated for 3 d in the dark on SH induction medium containing 288 mg/L Pro, 53 mg/L thioproline, 4.35 g/L K2SO4, and 100 μm acetosyringinone. The explants are washed in half-strength Murashige-Skoog medium (Murashige and Skoog, 1962) and plated on the same SH induction medium without acetosyringinone but with a suitable selection agent and suitable antibiotic to inhibit Agrobacterium growth. After several weeks, somatic embryos are transferred to BOi2Y development medium containing no growth regulators, no antibiotics, and 50 g/L sucrose. Somatic embryos are subsequently germinated on half-strength Murashige-Skoog medium. Rooted seedlings were transplanted into pots and grown in a greenhouse. T1 seeds are produced from plants that exhibit tolerance to the selection agent and that contain a single copy of the T-DNA insert.

Example 39 Evaluation Procedure 39.1 Evaluation Setup

Approximately 30 independent T0 rice transformants were generated. The primary transformants were transferred from a tissue culture chamber to a greenhouse for growing and harvest of T1 seed. Seven events, of which the T1 progeny segregated 3:1 for presence/absence of the transgene, were retained. For each of these events, approximately 10 T1 seedlings containing the transgene (hetero- and homo-zygotes) and approximately 10 T1 seedlings lacking the transgene (nullizygotes) were selected by monitoring visual marker expression. The transgenic plants and the corresponding nullizygotes were grown side-by-side at random positions. Greenhouse conditions were of shorts days (12 hours light), 28° C. in the light and 22° C. in the dark, and a relative humidity of 70%.

Four T1 events were further evaluated in the T2 generation following the same evaluation procedure as for the T1 generation but with more individuals per event. From the stage of sowing until the stage of maturity the plants were passed several times through a digital imaging cabinet. At each time point digital images (2048×1536 pixels, 16 million colours) were taken of each plant from at least 6 different angles.

39.2 Statistical Analysis: t-Test and F-Test

A two factor ANOVA (analysis of variants) was used as a statistical model for the overall evaluation of plant phenotypic characteristics. An F-test was carried out on all the parameters measured of all the plants of all the events transformed with the gene of the present invention. The F-test was carried out to check for an effect of the gene over all the transformation events and to verify for an overall effect of the gene, also known as a global gene effect. The threshold for significance for a true global gene effect was set at a 5% probability level for the F-test. A significant F-test value points to a gene effect, meaning that it is not only the mere presence or position of the gene that is causing the differences in phenotype.

To check for an effect of the genes within an event, i.e., for a line-specific effect, a t-test was performed within each event using data sets from the transgenic plants and the corresponding null plants. “Null plants” or “null segregants” or “nullizygotes” are the plants treated in the same way as the transgenic plant, but from which the transgene has segregated. Null plants can also be described as the homozygous negative transformed plants. The threshold for significance for the t-test is set at 10% probability level. The results for some events can be above or below this threshold. This is based on the hypothesis that a gene might only have an effect in certain positions in the genome, and that the occurrence of this position-dependent effect is not uncommon. This kind of gene effect is also named herein a “line effect of the gene”. The p-value is obtained by comparing the t-value to the t-distribution or alternatively, by comparing the F-value to the F-distribution. The p-value then gives the probability that the null hypothesis (i.e., that there is no effect of the transgene) is correct.

Example 40 Evaluation Results

Early vigour was determined by counting the total number of pixels from aboveground plant parts discriminated from the background. This value was averaged for the pictures taken on the same time point from different angles and was converted to a physical surface value expressed in square mm by calibration. The results described below are for plants three weeks post-germination.

Early vigour (as determined by aboveground area) was seen in six out of seven events of the T1 generation, with an overall increase in aboveground area for transgenic seedlings of 22% compared to control plants. Four of these T1 events were further evaluated in the T2 generation, and all four of these events gave an increase in aboveground area for transgenic seedlings compared to control plants, with an overall increase in aboveground area for transgenic seedlings of 13% compared to control plants. The results were also shown to be statistically significant with the p-value from the F-test being 0.0007 (T2 generation) indicating that the effect seen is likely due to the transgene rather than the position of the gene or a line effect.

Example Section F SPL15 Example 41 Identification of Sequences Related to the Nucleic Acid Sequence Used in the Methods of the Invention

Sequences (full length cDNA, ESTs or genomic) related to the nucleic acid sequence used in the methods of the present invention were identified amongst those maintained in the Entrez Nucleotides database at the National Center for Biotechnology Information using database sequence search tools, such as the Basic Local Alignment Tool (BLAST) (Altschul et al. (1990) J. Mol. Biol. 215:403-410; and Altschul et al. (1997) Nucleic Acids Res. 25:3389-3402). The program is used to find regions of local similarity between sequences by comparing nucleic acid or polypeptide sequences to sequence databases and by calculating the statistical significance of matches. The polypeptide encoded by the nucleic acid of the present invention was used for the TBLASTN algorithm, with default settings and the filter to ignore low complexity sequences set off. The output of the analysis was viewed by pairwise comparison, and ranked according to the probability score (E-value), where the score reflect the probability that a particular alignment occurs by chance (the lower the E-value, the more significant the hit). In addition to E-values, comparisons were also scored by percentage identity. Percentage identity refers to the number of identical nucleotides (or amino acids) between the two compared nucleic acid (or polypeptide) sequences over a particular length. In some instances, the default parameters may be adjusted to modify the stringency of the search

The Table N below provides a list of nucleic acid sequences related to the nucleic acid sequence used in the methods of the present invention.

TABLE N nucleic acid sequences related to the nucleic acid sequence (SEQ ID NO: 234) used in the methods of the present invention, and the corresponding deduced polypeptides Nucleic acid Polypeptide Sequence NCBI accession Name SEQ ID NO SEQ ID NO length number Source organism Arath_SPL15 234 235 Full length NM_115654.1 Arabidopsis thaliana (At3g57920) Arath_SPL9 236 237 Full length AY150378 Arabidopsis thaliana (At2g42200) Aqufo_SPL 238 239 Full length contig of DR915312 Aquilegia formosa × DR949057.1 Aquilegia pubescens Goshi_SPL 240 241 Full length DT566400 Gossypium hirsutum Iponi_SPL 242 243 Full length contig of Ipomoea nil BJ576204.1 BJ556115 BJ567301 Lacsa_SPL 244 245 Full length contig of DY966949 Lactuca sativa DW119178 Maldo_SPL 246 247 Full length contig of Malus domestica CN891102.1 CO868185.1 CV523507 Medtr_SPL 248 249 Full length spliced from Medicago truncatula AC170989.2 Nicbe_SPL 250 251 Full length contig of CK284078.1 Nicotiana CK294165 bentamiana Orysa_SPL 252 253 Full length XM_483285 Oryza sativa Orysa_SPL II 254 255 Full length spliced from AC108762 Oryza sativa Soltu_SPL 256 257 Full length contig of CK246692.1 Solanum tuberosum CK254420.1 Vitvi_SPL 258 259 Full length contig of Vitis vinifera CV098277 CV092812.1 Zeama_SPL 260 261 Full length contig of EB160653 Zea mays DY235599 DV029129 Zeama_SPL 262 263 Full length contig of AJ011619 Zea mays II DV033513.1 DY532686.1 Sorpr_SPL 264 265 Partial BF422188 Sorghum propinquium Allce_SPL 266 267 Partial CF444518.1 Allium cepa Antma_SPL 268 269 Partial AMA011623 Antirrhinum majus Brana_SPL 270 271 Partial CX189447 Brassica napus Sacof_SPL 272 273 Partial contig of CA113070 Saccharum CA254724 officinarum Fesar_SPL 274 275 Partial DT706587.1 Festuca arundinacea Brara_SPL 282 283 Full length AC189445.1 Brassica rapa Glyma_SPL 284 285 Full length CX708501.1 Glycine max BG651519.1 Poptr_SPL 286 287 Full length scaff_XVI.416 Populus tremuloides Citcl_SPL 288 289 Partial DY293795 Citrus clementina Betvu_SPL 290 291 Partial BQ594361.1 Beta vulgaris Hevbr_SPL 292 293 Partial EC604947 Hevea brasiliensis

Example 42 Determination of Global Similarity and Identity Between SPL15 Transcription Factors, and their SPL DBD

Global percentages of similarity and identity between SPL15 transcription factors were determined using one of the methods available in the art, the MatGAT (Matrix Global Alignment Tool) software (BMC Bioinformatics. 2003 4:29. MatGAT: an application that generates similarity/identity matrices using protein or DNA sequences. Campanella J J, Bitincka L, Smalley J; software hosted by Ledion Bitincka). MatGAT software generates similarity/identity matrices for DNA or protein sequences without needing pre-alignment of the data. The program performs a series of pair-wise alignments using the Myers and Miller global alignment algorithm (with a gap opening penalty of 12, and a gap extension penalty of 2), calculates similarity and identity using for example Blosum 62 (for polypeptides), and then places the results in a distance matrix. Sequence similarity is shown in the bottom half of the dividing line and sequence identity is shown in the top half of the diagonal dividing line. The sequence of SEQ ID NO: 235 is indicated as number 5 in the matrix.

Parameters used in the comparison were:

-   -   Scoring matrix: Blosum62     -   First Gap: 12     -   Extending gap: 2

Results of the software analysis are shown in Table 0 for the global similarity and identity over the full length of the SPL15 transcription factor polypeptides. Percentage identity is given above the diagonal and percentage similarity is given below the diagonal. Percentage identity between the SPL15 transcription factor paralogues and orthologues ranges between 30 and 70%, reflecting the relatively low sequence identity conservation between them outside of the SPL DBD.

TABLE O MatGAT results for global similarity and identity over the full length of the SPL15 transcription factor polypeptides. Global similarity and identity over the full length of the SPL15 transcription factor polypeptides 1 2 3 4 5 6 7 8 9 10 11 12 13 14  1. Arath_SPL9 51.1 44.8 40.3 38.4 44 43.1 40.3 34.6 35.9 39.4 46.7 33.9 35.7  2. Arath_SPL15 63.2 39.4 39 33.7 40.1 40.3 35.1 31.3 33.7 36.5 39.6 30.5 31.9  3. Goshi_SPL 58.9 53.2 47.3 43 54.4 46.9 52 41.3 40.2 50.1 59.8 39.5 39.1  4. Iponi_SPL 53.3 55.9 61.7 43.9 50.9 46.8 56.1 33.6 37.2 56.7 53.5 36.3 38.7  5. Lacsa_SPL 52 49.4 53.2 61.3 45.8 43.5 46.4 37 38.3 47.9 48.1 37.6 39.9  6. Maldo_SPL 59.3 54.5 64.3 63.5 56.3 49.5 57.4 42 38.1 55.2 68.7 38.9 40.6  7. Medtr_SPL 55.2 57.6 60.4 64.5 58.4 65.1 46.7 37.3 39.2 46.3 55.4 37.6 39.7  8. Nicbe_SPL 58.2 51.6 63.8 66.8 56.8 70.8 62.9 36.9 40 66.6 62.1 38.2 37.5  9. Orysa_SPL 48.7 42.2 54.2 47 47.2 53.2 49.2 51.8 62.4 37.3 40.7 59.5 54.9 10. Orysa_SPL II 49.9 45.8 53.4 49.1 48.9 51.1 53.4 53.2 72.2 37.6 43.6 54.3 62.9 11. Soltu_SPL 57.3 54 64 68.5 59.4 69.6 62.9 77.6 51.8 50.4 60.7 36.9 37.9 12. Vitvi_SPL 62.8 54.9 69.2 66 59.4 80.2 67.5 73.4 53.5 56.5 73.6 42.2 40.8 13. Zeama_SPL 47.3 43.3 55.2 48.8 49.3 52 51.2 52.5 68.3 67.9 49.8 54 54.9 14. Zeama_SPL II 49.2 43.1 53.2 51.6 50.8 54.5 53.2 48.7 64.3 71.2 51.1 54.6 66.2

Results of the software analysis are shown in Table P for the global similarity and identity over the SPL DBD of the SPL15 transcription factor polypeptides. Percentage identity is given above the diagonal and percentage similarity is given below the diagonal. Percentage identity between the SPL DBD of SPL15 transcription factor paralogues and orthologues ranges between 70% and 100%.

TABLE P MatGAT results for global similarity and identity over the SPL DBD of the SPL15 transcription factor polypeptides. Global similarity and identity over the SPL DBD of the SPL15 transcription factor polypeptides 1 2 3 4 5 6 7 8 9 10 11 12 13 14  1. SPL\DBD\Aqufo_SPL 75.6 79.5 84.8 85.9 87.2 85.9 88.5 84.6 80.8 78.2 85.9 91 76.9  2. SPL\DBD\Arath_SPL15 82.1 78.2 83.5 82.1 78.2 76.9 78.2 79.5 71.8 74.4 79.5 79.5 71.8  3. SPL\DBD\Arath_SPL9 87.2 85.9 77.2 78.2 82.1 82.1 79.5 78.2 76.9 78.2 79.5 80.8 76.9  4. SPL\DBD\Goshi_SPL 88.6 91.1 86.1 86.1 84.8 84.8 84.8 84.8 78.5 78.5 86.1 89.9 78.5  5. SPL\DBD\Iponi_SPL 89.7 85.9 87.2 91.1 84.6 84.6 85.9 85.9 80.8 79.5 87.2 89.7 78.2  6. SPL\DBD\Lacsa_SPL 89.7 85.9 88.5 91.1 91 88.5 84.6 85.9 80.8 79.5 85.9 89.7 78.2  7. SPL\DBD\Maldo_SPL 92.3 82.1 88.5 89.9 91 91 84.6 89.7 85.9 83.3 88.5 91 80.8  8. SPL\DBD\Medtr_SPL 89.7 85.9 89.7 92.4 92.3 91 93.6 84.6 79.5 78.2 88.5 93.6 78.2  9. SPL\DBD\Nicbe_SPL 87.2 83.3 85.9 88.6 92.3 89.7 91 92.3 84.6 82.1 88.5 89.7 80.8 10. SPL\DBD\Orysa_SPL 87.2 80.8 84.6 84.8 88.5 85.9 89.7 85.9 89.7 85.9 84.6 83.3 83.3 11. SPL\DBD\Orysa_SPL II 84.6 82.1 87.2 83.5 85.9 84.6 88.5 85.9 88.5 92.3 82.1 82.1 84.6 12. SPL\DBD\Soltu_SPL 89.7 87.2 87.2 91.1 94.9 89.7 93.6 93.6 92.3 87.2 84.6 93.6 80.8 13. SPL\DBD\Vitvi_SPL 92.3 87.2 89.7 93.7 94.9 92.3 96.2 97.4 92.3 87.2 87.2 96.2 82.1 14. SPL\DBD\Zeama_SPL II 83.3 79.5 84.6 83.5 84.6 83.3 84.6 87.2 84.6 88.5 89.7 83.3 85.9

Example 43 Cloning of the Nucleic Acid Sequence Used in the Methods of the Invention

DNA manipulation: unless otherwise stated, recombinant DNA techniques are performed according to standard protocols described in (Sambrook (2001) Molecular Cloning: a laboratory manual, 3rd Edition Cold Spring Harbor Laboratory Press, CSH, New York) or in Volumes 1 and 2 of Ausubel et al. (1994), Current Protocols in Molecular Biology, Current Protocols. Standard materials and methods for plant molecular work are described in Plant Molecular Biology Labfase (1993) by R.D.D. Croy, published by BIOS Scientific Publications Ltd (UK) and Blackwell Scientific Publications (UK).

The nucleic acid sequence used in the methods of the invention was amplified by PCR using as template a custom-made Arabidopsis thaliana mixed tissues cDNA library (in pCMV Sport 6.0; Invitrogen, Paisley, UK). PCR was performed using Hifi Taq DNA polymerase in standard conditions, using 200 ng of template in a 50 μl PCR mix. The primers used were prm07277 (SEQ ID NO: 280; sense, start codon in bold, AttB1 site in lower case: 5′-ggggacaagtttgtacaaaaaagcaggcttaaacaATGGAGTTGTTAATGTGTTCG 3′) and prm07278 (SEQ ID NO: 281; reverse, complementary, AttB2 site in lower case: 5′ ggggaccactttgtacaagaaagctgggtTGATGAAGATCTTAAAAGGTGA 3′), which include the AttB sites for Gateway recombination. The amplified PCR fragment was purified also using standard methods. The first step of the Gateway procedure, the BP reaction, was then performed, during which the PCR fragment recombines in vivo with the pDONR201 plasmid to produce, according to the Gateway terminology, an “entry clone”, pSPL15. Plasmid pDONR201 was purchased from Invitrogen, as part of the Gateway® technology.

Example 44 Expression Vector Construction

The entry clone p13075 was subsequently used in an LR reaction with p06659, a destination vector used for Oryza sativa transformation. This vector contains as functional elements within the T-DNA borders: a plant selectable marker; a screenable marker expression cassette; and a Gateway cassette intended for LR in vivo recombination with the nucleic acid sequence of interest already cloned in the entry clone. A rice HMGB promoter (SEQ ID NO: 294) for constitutive expression was located upstream of this Gateway cassette. Alternatively, the HMGB promoter represented by SEQ ID NO: 46 is equally useful. A similar construct was made with the SPL15 coding sequence under control of the constitutive GOS2 promoter (SEQ ID NO: 295).

After the LR recombination step, the resulting expression vector pHMGB::SPL15 (FIG. 26), or pGOS2::SPL15, was transformed into Agrobacterium strain LBA4044 and subsequently to Oryza sativa plants.

Example 45 Plant Transformation Rice Transformation

The Agrobacterium containing the expression vector was used to transform Oryza sativa plants. Mature dry seeds of the rice japonica cultivar Nipponbare were dehusked. Sterilization was carried out by incubating for one minute in 70% ethanol, followed by 30 minutes in 0.2% HgCl₂, followed by a 6 times 15 minutes wash with sterile distilled water. The sterile seeds were then germinated on a medium containing 2,4-D (callus induction medium). After incubation in the dark for four weeks, embryogenic, scutellum-derived calli were excised and propagated on the same medium. After two weeks, the calli were multiplied or propagated by subculture on the same medium for another 2 weeks. Embryogenic callus pieces were sub-cultured on fresh medium 3 days before co-cultivation (to boost cell division activity).

Agrobacterium strain LBA4404 containing the expression vector was used for co-cultivation. Agrobacterium was inoculated on AB medium with the appropriate antibiotics and cultured for 3 days at 28° C. The bacteria were then collected and suspended in liquid co-cultivation medium to a density (OD₆₀₀) of about 1. The suspension was then transferred to a Petri dish and the calli immersed in the suspension for 15 minutes. The callus tissues were then blotted dry on a filter paper and transferred to solidified, co-cultivation medium and incubated for 3 days in the dark at 25° C. Co-cultivated calli were grown on 2,4-D-containing medium for 4 weeks in the dark at 28° C. in the presence of a selection agent. During this period, rapidly growing resistant callus islands developed. After transfer of this material to a regeneration medium and incubation in the light, the embryogenic potential was released and shoots developed in the next four to five weeks. Shoots were excised from the calli and incubated for 2 to 3 weeks on an auxin-containing medium from which they were transferred to soil. Hardened shoots were grown under high humidity and short days in a greenhouse.

Approximately 35 independent T0 rice transformants were generated for one construct. The primary transformants were transferred from a tissue culture chamber to a greenhouse. After a quantitative PCR analysis to verify copy number of the T-DNA insert, only single copy transgenic plants that exhibit tolerance to the selection agent were kept for harvest of T1 seed. Seeds were then harvested three to five months after transplanting. The method yielded single locus transformants at a rate of over 50% (Aldemita and Hodges1996, Chan et al. 1993, Hiei et al. 1994).

Corn Transformation

Transformation of maize (Zea mays) is performed with a modification of the method described by Ishida et al. (1996) Nature Biotech 14(6): 745-50. Transformation is genotype-dependent in corn and only specific genotypes are amenable to transformation and regeneration. The inbred line A188 (University of Minnesota) or hybrids with A188 as a parent are good sources of donor material for transformation, but other genotypes can be used successfully as well. Ears are harvested from corn plant approximately 11 days after pollination (DAP) when the length of the immature embryo is about 1 to 1.2 mm. Immature embryos are cocultivated with Agrobacterium tumefaciens containing the expression vector, and transgenic plants are recovered through organogenesis. Excised embryos are grown on callus induction medium, then maize regeneration medium, containing the selection agent (for example imidazolinone but various selection markers can be used). The Petri plates are incubated in the light at 25° C. for 2-3 weeks, or until shoots develop. The green shoots are transferred from each embryo to maize rooting medium and incubated at 25° C. for 2-3 weeks, until roots develop. The rooted shoots are transplanted to soil in the greenhouse. T1 seeds are produced from plants that exhibit tolerance to the selection agent and that contain a single copy of the T-DNA insert.

Wheat Transformation

Transformation of wheat is performed with the method described by Ishida et al. (1996) Nature Biotech 14(6): 745-50. The cultivar Bobwhite (available from CIMMYT, Mexico) is commonly used in transformation. Immature embryos are co-cultivated with Agrobacterium tumefaciens containing the expression vector, and transgenic plants are recovered through organogenesis. After incubation with Agrobacterium, the embryos are grown in vitro on callus induction medium, then regeneration medium, containing the selection agent (for example imidazolinone but various selection markers can be used). The Petri plates are incubated in the light at 25° C. for 2-3 weeks, or until shoots develop. The green shoots are transferred from each embryo to rooting medium and incubated at 25° C. for 2-3 weeks, until roots develop. The rooted shoots are transplanted to soil in the greenhouse. T1 seeds are produced from plants that exhibit tolerance to the selection agent and that contain a single copy of the T-DNA insert.

Soybean Transformation

Soybean is transformed according to a modification of the method described in the Texas A&M U.S. Pat. No. 5,164,310. Several commercial soybean varieties are amenable to transformation by this method. The cultivar Jack (available from the Illinois Seed foundation) is commonly used for transformation. Soybean seeds are sterilised for in vitro sowing. The hypocotyl, the radicle and one cotyledon are excised from seven-day old young seedlings. The epicotyl and the remaining cotyledon are further grown to develop axillary nodes. These axillary nodes are excised and incubated with Agrobacterium tumefaciens containing the expression vector. After the cocultivation treatment, the explants are washed and transferred to selection media. Regenerated shoots are excised and placed on a shoot elongation medium. Shoots no longer than 1 cm are placed on rooting medium until roots develop. The rooted shoots are transplanted to soil in the greenhouse. T1 seeds are produced from plants that exhibit tolerance to the selection agent and that contain a single copy of the T-DNA insert.

Rapeseed/Canola Transformation

Cotyledonary petioles and hypocotyls of 5-6 day old young seedling are used as explants for tissue culture and transformed according to Babic et al. (1998, Plant Cell Rep 17: 183-188). The commercial cultivar Westar (Agriculture Canada) is the standard variety used for transformation, but other varieties can also be used. Canola seeds are surface-sterilized for in vitro sowing. The cotyledon petiole explants with the cotyledon attached are excised from the in vitro seedlings, and inoculated with Agrobacterium (containing the expression vector) by dipping the cut end of the petiole explant into the bacterial suspension. The explants are then cultured for 2 days on MSBAP-3 medium containing 3 mg/l BAP, 3% sucrose, 0.7% Phytagar at 23° C., 16 hr light. After two days of co-cultivation with Agrobacterium, the petiole explants are transferred to MSBAP-3 medium containing 3 mg/l BAP, cefotaxime, carbenicillin, or timentin (300 mg/l) for 7 days, and then cultured on MSBAP-3 medium with cefotaxime, carbenicillin, or timentin and selection agent until shoot regeneration. When the shoots are 5-10 mm in length, they are cut and transferred to shoot elongation medium (MSBAP-0.5, containing 0.5 mg/l BAP). Shoots of about 2 cm in length are transferred to the rooting medium (MS0) for root induction. The rooted shoots are transplanted to soil in the greenhouse. T1 seeds are produced from plants that exhibit tolerance to the selection agent and that contain a single copy of the T-DNA insert.

Alfalfa Transformation

A regenerating clone of alfalfa (Medicago sativa) is transformed using the method of (McKersie et al., 1999 Plant Physiol 119: 839-847). Regeneration and transformation of alfalfa is genotype dependent and therefore a regenerating plant is required. Methods to obtain regenerating plants have been described. For example, these can be selected from the cultivar Rangelander (Agriculture Canada) or any other commercial alfalfa variety as described by Brown D C W and A Atanassov (1985. Plant Cell Tissue Organ Culture 4: 111-112). Alternatively, the RA3 variety (University of Wisconsin) has been selected for use in tissue culture (Walker et al., 1978 Am J Bot 65:654-659). Petiole explants are cocultivated with an overnight culture of Agrobacterium tumefaciens C58C1 pMP90 (McKersie et al., 1999 Plant Physiol 119: 839-847) or LBA4404 containing the expression vector. The explants are cocultivated for 3 d in the dark on SH induction medium containing 288 mg/L Pro, 53 mg/L thioproline, 4.35 g/L K2SO4, and 100 μm acetosyringinone. The explants are washed in half-strength Murashige-Skoog medium (Murashige and Skoog, 1962) and plated on the same SH induction medium without acetosyringinone but with a suitable selection agent and suitable antibiotic to inhibit Agrobacterium growth. After several weeks, somatic embryos are transferred to BOi2Y development medium containing no growth regulators, no antibiotics, and 50 g/L sucrose. Somatic embryos are subsequently germinated on half-strength Murashige-Skoog medium. Rooted seedlings were transplanted into pots and grown in a greenhouse. T1 seeds are produced from plants that exhibit tolerance to the selection agent and that contain a single copy of the T-DNA insert.

Example 46 Evaluation Procedure 46.1 Evaluation Setup

Approximately 35 independent T0 rice transformants were generated. The primary transformants were transferred from a tissue culture chamber to a greenhouse for growing and harvest of T1 seed. Seven events, of which the T1 progeny segregated 3:1 for presence/absence of the transgene, were retained. For each of these events, approximately 10 T1 seedlings containing the transgene (hetero- and homo-zygotes) and approximately 10 T1 seedlings lacking the transgene (nullizygotes) were selected by monitoring visual marker expression. The transgenic plants and the corresponding nullizygotes were grown side-by-side at random positions. Greenhouse conditions were of shorts days (12 hours light), 28° C. in the light and 22° C. in the dark, and a relative humidity of 70%.

Five T1 events were further evaluated in the T2 generation following the same evaluation procedure as for the T1 generation but with more individuals per event. From the stage of sowing until the stage of maturity the plants were passed several times through a digital imaging cabinet. At each time point digital images (2048×1536 pixels, 16 million colours) were taken of each plant from at least 6 different angles.

The early vigour is the plant (seedling) aboveground area three weeks post-germination. Increase in root biomass is expressed as an increase in total root biomass (measured as maximum biomass of roots observed during the lifespan of a plant); or as an increase in the root/shoot index (measured as the ratio between root mass and shoot mass in the period of active growth of root and shoot).

46.2 Statistical Analysis: F-Test

A two factor ANOVA (analysis of variants) was used as a statistical model for the overall evaluation of plant phenotypic characteristics. An F-test was carried out on all the parameters measured of all the plants of all the events transformed with the gene of the present invention. The F-test was carried out to check for an effect of the gene over all the transformation events and to verify for an overall effect of the gene, also known as a global gene effect. The threshold for significance for a true global gene effect was set at a 5% probability level for the F-test. A significant F-test value points to a gene effect, meaning that it is not only the mere presence or position of the gene that is causing the differences in phenotype.

To check for an effect of the genes within an event, i.e., for a line-specific effect, a t-test was performed within each event using data sets from the transgenic plants and the corresponding null plants. “Null plants” or “null segregants” or “nullizygotes” are the plants treated in the same way as the transgenic plant, but from which the transgene has segregated. Null plants can also be described as the homozygous negative transformed plants. The threshold for significance for the t-test is set at 10% probability level. The results for some events can be above or below this threshold. This is based on the hypothesis that a gene might only have an effect in certain positions in the genome, and that the occurrence of this position-dependent effect is not uncommon. This kind of gene effect is also named herein a “line effect of the gene”. The p-value is obtained by comparing the t-value to the t-distribution or alternatively, by comparing the F-value to the F-distribution. The p-value then gives the probability that the null hypothesis (i.e., that there is no effect of the transgene) is correct.

Example 47 Evaluation Results

The plant aboveground area (or leafy biomass) was determined by counting the total number of pixels on the digital images from aboveground plant parts discriminated from the background. This value was averaged for the pictures taken on the same time point from the different angles and was converted to a physical surface value expressed in square mm by calibration. Experiments show that the aboveground plant area measured this way correlates with the biomass of plant parts above ground. The above ground area is the time point at which the plant had reached its maximal leafy biomass.

The mature primary panicles were harvested, counted, bagged, barcode-labeled and then dried for three days in an oven at 37° C. The panicles were then threshed and all the seeds were collected and counted. The filled husks were separated from the empty ones using an air-blowing device. The empty husks were discarded and the remaining fraction was counted again. The filled husks were weighed on an analytical balance. The number of filled seeds was determined by counting the number of filled husks that remained after the separation step. The total seed yield was measured by weighing all filled husks harvested from a plant. Total seed number per plant was measured by counting the number of husks harvested from a plant. Thousand kernel weight (TKW) is extrapolated from the number of filled seeds counted and their total weight. The harvest index (HI) in the present invention is defined as the ratio between the total seed yield and the above ground area (mm²), multiplied by a factor 10⁶. The total number of flowers per panicle as defined in the present invention is the ratio between the total number of seeds and the number of mature primary panicles. The seed fill rate as defined in the present invention is the proportion (expressed as a %) of the number of filled seeds over the total number of seeds (or florets).

As presented in Tables Q to W, the aboveground biomass, the number of flowers per panicle, the seed yield, the total number of seeds, the number of filled seeds, the thousand kernel weight (TKW) and harvest index are increased in the transgenic plants with increased expression a nucleic acid encoding a SPL15 transcription factor polypeptide, compared to suitable control plants. Results from the T1 and the T2 generations are shown.

Table Q shows the number of transgenic events with an increase in aboveground biomass, the percentage of this increase, as well as the statistical relevance of this increase according to the F-test.

TABLE Q Number of transgenic events with an increase in aboveground biomass, the percentage of the increase, and P value of the F-test in T1 and T2 generation of transgenic rice with increased expression of a nucleic acid encoding an SPL15 transcription factor polypeptide. Aboveground biomass Number of events showing an increase % Difference P value of F test T1 generation 5 out of 7 5 0.0773 T2 generation 4 out of 5 7 0.0172

Table R shows the number of transgenic events with an increase in the total number of flowers per panicle, the percentage of this increase, as well as the statistical relevance of this increase according to the F-test.

TABLE R Number of transgenic events with an increase in flowers per panicle, the percentage of the increase, and P value of the F-test in T1 and T2 generation of transgenic rice with increased expression of a nucleic acid encoding an SPL15 transcription factor polypeptide. Flowers per panicle Number of events showing an increase % Difference P value of F test T1 generation 6 out of 7 4 0.0447 T2 generation 4 out of 5 10 0.0013

Table S shows the number of transgenic events with an increase in total seed yield (total seed weight), the percentage of this increase, as well as the statistical relevance of this increase according to the F-test.

TABLE S Number of transgenic events with an increase in seed yield, the percentage of the increase, and P value of the F-test in T1 and T2 generation of transgenic rice with increased expression of a nucleic acid encoding an SPL15 transcription factor polypeptide. Seed yield Number of events showing an increase % Difference P value of F test T1 generation 7 out of 7 15 0.0019 T2 generation 5 out of 5 21 0.0001

Table T shows the number of transgenic events with an increase in the total number of seeds, the percentage of this increase, as well as the statistical relevance of this increase according to the F-test.

TABLE T Number of transgenic events with an increase in total number of seeds, the percentage of the increase, and P value of the F-test in T1 and T2 generation of transgenic rice with increased expression of a nucleic acid encoding an SPL15 transcription factor polypeptide. Total number of seeds Number of events showing an increase % Difference P value of F test T1 generation 6 out of 7 6 0.07 T2 generation 4 out of 5 13 0.0023

Table U shows the number of transgenic events with an increase in the number of filled seeds, the percentage of this increase, as well as the statistical relevance of this increase according to the F-test.

TABLE U Number of transgenic events with an increase in number of filled seeds, the percentage of the increase, and P value of the F-test in T1 and T2 generation of transgenic rice with increased expression of a nucleic acid encoding an SPL15 transcription factor polypeptide. Number of filled seeds Number of events showing an increase % Difference P value of F test T1 generation 6 out of 7 14 0.0031 T2 generation 4 out of 5 19 0.0003

Table V shows the number of transgenic events with an increase in the harvest index, the percentage of this increase, as well as the statistical relevance of this increase according to the F-test.

TABLE V Number of transgenic events with an increase in harvest index, the percentage of the increase, and P value of the F-test in T1 and T2 generation of transgenic rice with increased expression of a nucleic acid encoding an SPL15 transcription factor polypeptide. Harvest index Number of events showing an increase % Difference P value of F test T1 generation 7 out of 7 12 0.0003 T2 generation 4 out of 5 15 0.0001

Table W shows the number of transgenic events with an increase in the thousand kernel weight (TKW), the percentage of this increase, as well as the statistical relevance of this increase according to the F-test.

TABLE W Number of transgenic events with an increase in thousand kernel weight (TKW), the percentage of the increase, and P value of the F-test in T1 and T2 generation of transgenic rice with increased expression of a nucleic acid encoding an SPL15 transcription factor polypeptide. Thousand kernel weight Number of events showing an increase % Difference P value of F test T1 generation 4 out of 7 2 0.0041 T2 generation 4 out of 5 1 0.0259

Example 48 Results of the Phenotypic Evaluation of the Transgenic Plants Expressing SEQ ID NO: 234 Under the Control of a Constitutive Promoter

The results of the evaluation of transgenic rice plants expressing the nucleic acid sequence useful in performing the methods of the invention, under the control of the constitutive GOS2 promoter, are presented in Table X. The percentage difference between the transgenics and the corresponding nullizygotes is also shown.

The transgenic plants expressing the nucleic acid sequence useful in performing the methods of the invention, have increased early vigour and increased TKW compared to the control plants (in this case, the nullizygotes).

TABLE X Results of the evaluation of T1 generation transgenic rice plants expressing the nucleic acid sequence useful in performing the methods of the invention, under the control of a strong constitutive GOS2 promoter. % Increase of the Trait best events in T1 generation Increased early vigour 17% Total seed yield (per plant) 18% Total number of filled seeds 19% Increased seed fill rate 10% Increased harvest index 15% 

1. A method for enhancing a yield-related trait in a plant relative to a control plant, comprising: (a) increasing expression of: (i) a nucleic acid encoding a HAL3 polypeptide; (ii) a nucleic acid encoding a MADS15 protein; (iii) a nucleic acid encoding a PLT transcription factor polypeptide; (iv) a nucleic acid encoding an SPL15 transcription factor polypeptide; or (v) a nucleic acid encoding a bHLH transcription factor comprising the amino acid sequence of SEQ ID NO 213, SEQ ID NO 215, SEQ ID NO: 217, SEQ ID NO: 219, SEQ ID NO 225, SEQ ID NO: 297, SEQ ID NO: 299 or SEQ ID NO: 301, or an orthologue or paralogue thereof; (b) selecting for a plant having an enhanced yield-related trait relative to a control plant.
 2. The method of claim 1, wherein said increased expression is effected by: (a) introducing and expressing in the plant a nucleic acid encoding a HAL3 polypeptide; (b) introducing and expressing in the plant a nucleic acid encoding a MADS15 protein, wherein said MADS15 protein comprises any one or more of the motifs of SEQ ID NO: 48, SEQ ID NO: 49, SEQ ID NO: 50 and SEQ ID NO: 51; (c) introducing and expressing in the plant a nucleic acid encoding a PLT transcription factor polypeptide; (d) introducing and expressing in the plant a nucleic acid encoding a SPL15 transcription factor polypeptide; or (e) introducing and expressing in the plant a nucleic acid encoding a bHLH transcription factor comprising the amino acid sequence of SEQ ID NO 213, SEQ ID NO 215, SEQ ID NO: 217, SEQ ID NO: 219, SEQ ID NO 225, SEQ ID NO: 297, SEQ ID NO: 299 or SEQ ID NO: 301, or an orthologue or paralogue thereof.
 3. The method of claim 2, wherein: (a) said nucleic acid encoding a HAL3 protein comprises any one of the nucleic acid SEQ ID NOs given in Table A, or a portion thereof, or a sequence capable of hybridizing with any one of the nucleic acids SEQ ID NOs given in Table A; (b) said nucleic acid encoding a MADS15 protein comprises any one of the nucleic acid SEQ ID NOs given in Table D, or a portion thereof, or a sequence capable of hybridixing with any one of the nucleic acids SEQ ID NOs given in Table D; (c) said nucleic acid encoding a PLT transcription factor polypeptide comprises any one of the nucleic acid SEQ ID NOs given in Table I, or a portion thereof, or a sequence capable of hybridizing with any one of the nucleic acids SEQ ID NOs given in Table I; (d) said nucleic acid encoding a SPL15 transcription factor polypeptide comprises any one of the nucleic acid SEQ ID NOs given in Table N, or a portion thereof, or a sequence capable of hybridizing with any one of the nucleic acids SEQ ID NOs given in Table N; or (e) said nucleic acid encoding a bHLH transcription factor is a portion of, an allelic variant of, a splice variant of, or a sequence capable of hybridizing to a nucleic acid comprising the nucleotide sequence of SEQ ID NO: 212, SEQ ID NO: 214, SEQ ID NO: 216, SEQ ID NO: 218, SEQ ID NO: 220, SEQ ID NO: 222, SEQ ID NO: 224, SEQ ID NO: 226, SEQ ID NO: 228, SEQ ID NO: 296, SEQ ID NO: 298 or SEQ ID NO: 300, wherein said portion, allelic variant, splice variant or hybridizing sequence encodes a bHLH transcription factor.
 4. The method of claim 2, wherein: (a) said nucleic acid encoding a HAL3 protein encodes an orthologue or paralogue of any of the polypeptide SEQ ID NOs given in Table A; (b) said nucleic acid encoding a MADS15 protein encodes an orthologue or paralogue of any of the polypeptide SEQ ID NOs given in Table D; (c) said nucleic acid encoding a PLT transcription factor encodes an orthologue or paralogue of any of the polypeptide SEQ ID NOs given in Table D; (d) said nucleic acid encoding a SPL15 transcription factor polypeptide encodes an orthologue or paralogue of any of the polypeptide SEQ ID NOs given in Table N.
 5. The method of claim 1, wherein: (a) said nucleic acid encodes a HAL3 protein, and wherein said enhanced yield-related trait comprises increased yield and/or early vigour; (b) said nucleic acid encodes MADS15 protein, and wherein said enhanced yield-related trait comprises root biomass; (c) said nucleic acid encodes a PLT transcription factor, and wherein said enhanced yield-related trait comprises increased seed yield; (d) said nucleic acid encodes a SPL15 transcription factor polypeptide, and wherein said enhanced yield-related trait comprises increased seed yield; (e) said nucleic acid encodes a bHLH transcription factor, and wherein said enhanced yield-related trait comprises early vigour.
 6. The method of claim 5, wherein: (a) said nucleic acid encodes a HAL3 protein, and wherein said enhanced yield-related trait is increased seed yield comprising increased seed biomass, increased harvest index, and/or increased number of (filled) seeds; (b) said nucleic acid encodes a PLT transcription factor, and wherein said increased seed yield comprises increased seed biomass, increased number of flowers per plant, increased number of (filled) seeds, increased seed filling rate, increased harvest index, increased Thousand Kernel Weight (TKW), increased seed area, increased seed length, and/or increased seed width; (c) said nucleic acid encodes a SPL15 transcription factor polypeptide, and wherein said increased seed yield comprises increased aboveground biomass, increased number of flowers per plant, increased seed yield, increased number of (filled) seeds, increased thousand kernel weight (TKW), and/or increased harvest index.
 7. The method of claim 2, wherein: (a) said nucleic acid encoding a HAL3 protein protein is operably linked to a shoot-specific promoter or a beta expansin promoter; (b) said nucleic acid encoding a MADS15 protein is operably linked to a constitutive promoter or a GOS2 promoter; (c) said nucleic acid encoding a PLT transcription factor is operably linked to a constitutive promoter or a GOS2 promoter; (d) said nucleic acid encoding a SPL15 transcription factor polypeptide is operably linked to a constitutive promoter, a high mobility group B (HMGB) promoter, a GOS2 promoter, a rice HMGB promoter, or a rice GOS2 promoter; or (e) said nucleic acid encoding a bHLH transcription factor is operably linked to a constitutive promoter or a GOS2 promoter.
 8. The method of claim 2, wherein: (a) said nucleic acid encoding a HAL3 protein is of plant origin, from a dicotyledonous plant, from the family Brassicaceae, from the genus Arabidopsis, or from Arabidopsis thaliana; (b) said nucleic acid encoding a MADS15 protein is of plant origin, from a monocotyledonous plant, from the family Poaceae, from the genus Oryza, or from Oryza sativa; (c) said nucleic acid encoding a PLT transcription factor is of plant origin, from a dicotyledonous plant, from the Brassicaceae family, from the genus Arabidopsis, or from Arabidopsis thaliana; (d) said nucleic acid encoding a SPL15 transcription factor polypeptide is of plant origin, from a dicotyledonous plant, from the family Brassicaceae, or from Arabidopsis thaliana; or (e) said nucleic acid encoding a bHLH transcription factor is of plant origin, from a monocotyledonous plant, from the family Poaceae, from the genus Oryza, or from Oryza sativa.
 9. A plant or part thereof obtained by the method of claim 1, or a seed or progeny of said plant, wherein said plant or part thereof, or said seed or progeny, comprises a recombinant nucleic acid encoding a HAL3 polypeptide, a recombinant nucleic acid encoding a MADS15 protein, a recombinant nucleic acid encoding a PLT transcription factor polypeptide operably linked to a constitutive promoter, a recombinant nucleic acid encoding a SPL15 transcription factor polypeptide, or a recombinant nucleic acid encoding a bHLH transcription factor.
 10. A construct comprising: (a) (i) a nucleic acid encoding a HAL3 polypeptide (ii) a nucleic acid encoding a MADS15 protein comprising one or more of the motifs of SEQ ID NO: 48, SEQ ID NO: 49, SEQ ID NO: 50 and SEQ ID NO: 51; (iii) a nucleic acid encoding a PLT transcription factor polypeptide; (iv) a nucleic acid encoding an SPL15 transcription factor polypeptide; or (v) a nucleic acid encoding a bHLH transcription factor comprising the amino acid sequence of SEQ ID NO 213, SEQ ID NO 215, SEQ ID NO: 217, SEQ ID NO: 219, SEQ ID NO 225, SEQ ID NO: 297, SEQ ID NO: 299 or SEQ ID NO: 301, or an orthologue or paralogue thereof; (b) one or more control sequences capable of driving expression of the nucleic acid of (a) in a plant; and optionally (c) a transcription termination sequence.
 11. The construct of claim 10, wherein: (a) said nucleic acid encodes a HAL3 polypeptide, and wherein said one or more control sequences is a shoot-specific promoter or a beta expansin promoter; (b) said nucleic acid encodes a MADS15 protein, and wherein said one or more control sequences is a constitutive promoter or a GOS2 promoter; (c) said nucleic acid encodes a PLT transcription factor polypeptide, and wherein said one or more control sequences is a constitutive promoter or a GOS2 promoter; (d) said nucleic acid encodes a SPL15 transcription factor polypeptide, and wherein said one or more control sequences is a constitutive promoter, a HMGB promoter, or a GOS2 promoter; or (e) said nucleic acid encodes a bHLH transcription factor, and wherein said one or more control sequences is a constitutive promoter or a GOS2 promoter.
 12. A plant, plant part or plant cell transformed with the construct of claim
 10. 13. A plant, plant part or plant cell comprising the construct of claim
 10. 14. A method for the production of a transgenic plant having an enhanced yield-related trait relative to a control plant, comprising: (a) introducing and increasing expression in a plant of: (i) a nucleic acid encoding a HAL3 polypeptide; (ii) a nucleic acid encoding a MADS15 protein comprising one or more of the motifs of SEQ ID NO: 48, SEQ ID NO: 49, SEQ ID NO: 50 and SEQ ID NO: 51; (iii) a nucleic acid encoding a PLT transcription factor polypeptide; (iv) a nucleic acid encoding an SPL15 transcription factor polypeptide; or (v) a nucleic acid encoding a bHLH transcription factor comprising the amino acid sequence of SEQ ID NO 213, SEQ ID NO 215, SEQ ID NO: 217, SEQ ID NO: 219, SEQ ID NO 225, SEQ ID NO: 297, SEQ ID NO: 299 or SEQ ID NO: 301, or an orthologue or paralogue thereof; (b) cultivating the plant under conditions promoting plant growth and development; and (c) selecting for a plant having an enhanced yield-related trait relative to a control plant.
 15. The method of claim 14, further comprising obtaining a seed or progeny of said plant.
 16. A transgenic plant having an enhanced yield-related trait relative to a control plant resulting from increased expression of: (i) a nucleic acid encoding a HAL3 polypeptide; (ii) a nucleic acid encoding a MADS15 protein comprising one or more of the motifs of SEQ ID NO: 48, SEQ ID NO: 49, SEQ ID NO: 50 and SEQ ID NO: 51; (iii) a nucleic acid encoding a PLT transcription factor polypeptide; (iv) a nucleic acid encoding an SPL15 transcription factor polypeptide; or (v) a nucleic acid encoding a bHLH transcription factor comprising the amino acid sequence of SEQ ID NO 213, SEQ ID NO 215, SEQ ID NO: 217, SEQ ID NO: 219, SEQ ID NO 225, SEQ ID NO: 297, SEQ ID NO: 299 or SEQ ID NO: 301, or an orthologue or paralogue thereof, in said plant, or a transgenic plant cell obtained from said transgenic plant.
 17. The transgenic plant of claim 16, wherein said plant is a crop plant, a monocot plant or a cereal, or wherein said plant is rice, maize, wheat, barley, millet, rye, triticale, sorghum or oats.
 18. Harvestable parts of the transgenic plant of claim
 16. 19. Products obtained from the transgenic plant of claim 16 and/or from harvestable parts of said trasngenic plant.
 20. A method for increasing abiotic stress resistance in a plant relative to a control plant, comprising introducing into a plant the construct of claim 10, and selecting for a plant having increased abiotic stress resistance relative to a control plant, wherein said nucleic acid encodes a PLT transcription factor polypeptide, and wherein said increased abiotic stress resistance is preferably increased nutrient uptake efficiency.
 21. An isolated polypeptide comprising: (a) the amino acid sequence of SEQ ID NO: 297, SEQ ID NO: 299, or SEQ ID NO: 301; or (b) an amino acid sequence having at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or more sequence identity to the amino acid sequence of SEQ ID NO: 297, SEQ ID NO: 299 or SEQ ID NO: 301, wherein said amino acid sequence further comprises a bHLH domain.
 22. An isolated nucleic acid molecule comprising: (a) a nucleic acid sequence encoding the isolated polypeptide of claim 21; (b) the nucleic acid sequence of SEQ ID NO: 296, SEQ ID NO: 298 or SEQ ID NO: 300; or (c) the complement of the nucleic acid sequence of SEQ ID NO: 296, SEQ ID NO: 298 or SEQ ID NO:
 300. 